--- /tmp/kmer-0~20150903+r2013-8+b1lk9_3ub1/debian/sim4db_0~20150903+r2013-8+b1_amd64.deb
+++ sim4db_0~20150903+r2013-8+b1_amd64.deb
├── file list
│ @@ -1,3 +1,3 @@
│  -rw-r--r--   0        0        0        4 2020-11-18 23:57:22.000000 debian-binary
│ --rw-r--r--   0        0        0     2160 2020-11-18 23:57:22.000000 control.tar.xz
│ --rw-r--r--   0        0        0   436616 2020-11-18 23:57:22.000000 data.tar.xz
│ +-rw-r--r--   0        0        0     2164 2020-11-18 23:57:22.000000 control.tar.xz
│ +-rw-r--r--   0        0        0   436580 2020-11-18 23:57:22.000000 data.tar.xz
├── control.tar.xz
│ ├── control.tar
│ │ ├── ./md5sums
│ │ │ ├── ./md5sums
│ │ │ │┄ Files differ
├── data.tar.xz
│ ├── data.tar
│ │ ├── ./usr/bin/cleanPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 9cd56353ef8bf654131dc4f215b6340c6c688172
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: a2ccaa9d1e5bf5c5eb7092f18eb68651d5a6d377
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -120,15 +120,15 @@
│ │ │ │  ?char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -156,15 +156,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -236,15 +236,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -d56353ef8bf654131dc4f215b6340c6c688172.debug
│ │ │ │ +ccaa9d1e5bf5c5eb7092f18eb68651d5a6d377.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -101,15 +101,15 @@
│ │ │ │    0x0000c620 202d2d00 203c2d00 202d3e00 554e4b4e  --. <-. ->.UNKN
│ │ │ │    0x0000c630 4f574e00 6572726f 72006162 6f727465 OWN.error.aborte
│ │ │ │    0x0000c640 6400696e 74726163 7461626c 6500756e d.intractable.un
│ │ │ │    0x0000c650 6b6e6f77 6e007265 76657273 6500666f known.reverse.fo
│ │ │ │    0x0000c660 72776172 6400636f 6d706c65 6d656e74 rward.complement
│ │ │ │    0x0000c670 00000000 00000000 2f627569 6c642f6b ......../build/k
│ │ │ │    0x0000c680 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000c690 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000c690 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000c6a0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000c6b0 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x0000c6c0 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x0000c6d0 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x0000c6e0 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x0000c6f0 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x0000c700 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -235,15 +235,15 @@
│ │ │ │    0x0000ce80 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000ce90 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000cea0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000ceb0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000cec0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000ced0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000cee0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000cef0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000cef0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000cf00 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000cf10 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000cf20 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000cf30 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000cf40 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000cf50 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000cf60 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 64353633 35336566 38626636 35343133 d56353ef8bf65413
│ │ │ │ -  0x00000010 31646334 66323135 62363334 30633663 1dc4f215b6340c6c
│ │ │ │ -  0x00000020 36383831 37322e64 65627567 00000000 688172.debug....
│ │ │ │ -  0x00000030 d012205f                            .. _
│ │ │ │ +  0x00000000 63636161 39643165 35626635 63356562 ccaa9d1e5bf5c5eb
│ │ │ │ +  0x00000010 37303932 66313865 62363836 35316435 7092f18eb68651d5
│ │ │ │ +  0x00000020 61366433 37372e64 65627567 00000000 a6d377.debug....
│ │ │ │ +  0x00000030 28bd9268                            (..h
│ │ ├── ./usr/bin/comparePolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 9f9cd795bfb4251c2793f13d030debb600224fee
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: f582924a71b5d11d916c10bd74db2cfed78bdfa2
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -109,15 +109,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -154,15 +154,15 @@
│ │ │ │  Cs4p_compareExons()-- Can't allocate %u + %u words for counting exons.
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -234,15 +234,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -9cd795bfb4251c2793f13d030debb600224fee.debug
│ │ │ │ +82924a71b5d11d916c10bd74db2cfed78bdfa2.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -44,15 +44,15 @@
│ │ │ │    0x00010290 202d2d00 203c2d00 202d3e00 554e4b4e  --. <-. ->.UNKN
│ │ │ │    0x000102a0 4f574e00 6572726f 72006162 6f727465 OWN.error.aborte
│ │ │ │    0x000102b0 6400696e 74726163 7461626c 6500756e d.intractable.un
│ │ │ │    0x000102c0 6b6e6f77 6e007265 76657273 6500666f known.reverse.fo
│ │ │ │    0x000102d0 72776172 6400636f 6d706c65 6d656e74 rward.complement
│ │ │ │    0x000102e0 00000000 00000000 2f627569 6c642f6b ......../build/k
│ │ │ │    0x000102f0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00010300 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00010300 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00010310 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x00010320 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x00010330 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x00010340 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x00010350 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x00010360 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x00010370 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -205,15 +205,15 @@
│ │ │ │    0x00010ca0 41206c69 6e652061 74206279 74652025 A line at byte %
│ │ │ │    0x00010cb0 6c750a00 00000000 766f6964 2073696d lu......void sim
│ │ │ │    0x00010cc0 34706f6c 6973683a 3a733470 5f6c696e 4polish::s4p_lin
│ │ │ │    0x00010cd0 6573546f 506f6c69 73685334 44422875 esToPolishS4DB(u
│ │ │ │    0x00010ce0 696e7433 322c2075 696e7433 322c2063 int32, uint32, c
│ │ │ │    0x00010cf0 6861722a 2a2c2075 696e7433 322a2900 har**, uint32*).
│ │ │ │    0x00010d00 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00010d10 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00010d10 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00010d20 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x00010d30 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x00010d40 706f6c69 73682d73 7472696e 67746f70 polish-stringtop
│ │ │ │    0x00010d50 6f6c6973 682e4300 73696d34 706f6c69 olish.C.sim4poli
│ │ │ │    0x00010d60 73683a3a 7334705f 6c696e65 73546f50 sh::s4p_linesToP
│ │ │ │    0x00010d70 6f6c6973 68533444 4228292d 2d20496e olishS4DB()-- In
│ │ │ │    0x00010d80 76616c69 64207369 6d346462 20666f72 valid sim4db for
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 39636437 39356266 62343235 31633237 9cd795bfb4251c27
│ │ │ │ -  0x00000010 39336631 33643033 30646562 62363030 93f13d030debb600
│ │ │ │ -  0x00000020 32323466 65652e64 65627567 00000000 224fee.debug....
│ │ │ │ -  0x00000030 28ae0797                            (...
│ │ │ │ +  0x00000000 38323932 34613731 62356431 31643931 82924a71b5d11d91
│ │ │ │ +  0x00000010 36633130 62643734 64623263 66656437 6c10bd74db2cfed7
│ │ │ │ +  0x00000020 38626466 61322e64 65627567 00000000 8bdfa2.debug....
│ │ │ │ +  0x00000030 57a84aa6                            W.J.
│ │ ├── ./usr/bin/convertPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: ffc886ba6548dc11bf8292dcd5a25541566f5b44
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: fa85a8039358602987192ca7093d52e92eaf6fc5
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -93,15 +93,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -112,15 +112,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -193,15 +193,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -c886ba6548dc11bf8292dcd5a25541566f5b44.debug
│ │ │ │ +85a8039358602987192ca7093d52e92eaf6fc5.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -82,15 +82,15 @@
│ │ │ │    0x0000a4f0 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000a500 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000a510 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000a520 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000a530 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000a540 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000a550 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000a560 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000a560 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000a570 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000a580 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000a590 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000a5a0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000a5b0 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000a5c0 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000a5d0 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -153,15 +153,15 @@
│ │ │ │    0x0000a960 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000a970 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000a980 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000a990 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000a9a0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000a9b0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000a9c0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000a9d0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000a9d0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000a9e0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000a9f0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000aa00 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000aa10 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000aa20 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000aa30 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000aa40 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 63383836 62613635 34386463 31316266 c886ba6548dc11bf
│ │ │ │ -  0x00000010 38323932 64636435 61323535 34313536 8292dcd5a2554156
│ │ │ │ -  0x00000020 36663562 34342e64 65627567 00000000 6f5b44.debug....
│ │ │ │ -  0x00000030 e0119879                            ...y
│ │ │ │ +  0x00000000 38356138 30333933 35383630 32393837 85a8039358602987
│ │ │ │ +  0x00000010 31393263 61373039 33643532 65393265 192ca7093d52e92e
│ │ │ │ +  0x00000020 61663666 63352e64 65627567 00000000 af6fc5.debug....
│ │ │ │ +  0x00000030 7ae342ef                            z.B.
│ │ ├── ./usr/bin/convertToAtac
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 7d9d25c497401be28f44b8a5b4cc0e38ecf2b6b2
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: f0144271e6ca8c4c7d4f43097d3268969e1d170a
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -1,8 +1,9 @@
│ │ │ │  /lib64/ld-linux-x86-64.so.2
│ │ │ │ +L}OC	}2h
│ │ │ │  __gmon_start__
│ │ │ │  _ITM_deregisterTMCloneTable
│ │ │ │  _ITM_registerTMCloneTable
│ │ │ │  __gxx_personality_v0
│ │ │ │  _Unwind_Resume
│ │ │ │  __errno_location
│ │ │ │  __stpcpy_chk
│ │ │ │ @@ -103,15 +104,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -122,15 +123,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -203,15 +204,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -9d25c497401be28f44b8a5b4cc0e38ecf2b6b2.debug
│ │ │ │ +144271e6ca8c4c7d4f43097d3268969e1d170a.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -96,15 +96,15 @@
│ │ │ │    0x0000b5d0 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000b5e0 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000b5f0 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000b600 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000b610 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000b620 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000b630 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000b640 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000b640 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000b650 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000b660 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000b670 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000b680 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000b690 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000b6a0 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000b6b0 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -167,15 +167,15 @@
│ │ │ │    0x0000ba40 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000ba50 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000ba60 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000ba70 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000ba80 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000ba90 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000baa0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000bab0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000bab0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000bac0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000bad0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000bae0 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000baf0 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000bb00 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000bb10 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000bb20 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 39643235 63343937 34303162 65323866 9d25c497401be28f
│ │ │ │ -  0x00000010 34346238 61356234 63633065 33386563 44b8a5b4cc0e38ec
│ │ │ │ -  0x00000020 66326236 62322e64 65627567 00000000 f2b6b2.debug....
│ │ │ │ -  0x00000030 3a060511                            :...
│ │ │ │ +  0x00000000 31343432 37316536 63613863 34633764 144271e6ca8c4c7d
│ │ │ │ +  0x00000010 34663433 30393764 33323638 39363965 4f43097d3268969e
│ │ │ │ +  0x00000020 31643137 30612e64 65627567 00000000 1d170a.debug....
│ │ │ │ +  0x00000030 4767276d                            Gg'm
│ │ ├── ./usr/bin/convertToExtent
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 243b80d5b4fc4b50b93a0795860de9cc09907161
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: eb9bb33b15048f9f4918f0ccb3e39a2cbed89c99
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -113,15 +113,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -132,15 +132,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -212,15 +212,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -3b80d5b4fc4b50b93a0795860de9cc09907161.debug
│ │ │ │ +9bb33b15048f9f4918f0ccb3e39a2cbed89c99.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -112,15 +112,15 @@
│ │ │ │    0x0000a6d0 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000a6e0 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000a6f0 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000a700 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000a710 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000a720 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000a730 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000a740 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000a740 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000a750 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000a760 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000a770 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000a780 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000a790 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000a7a0 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000a7b0 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -183,15 +183,15 @@
│ │ │ │    0x0000ab40 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000ab50 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000ab60 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000ab70 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000ab80 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000ab90 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000aba0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000abb0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000abb0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000abc0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000abd0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000abe0 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000abf0 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000ac00 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000ac10 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000ac20 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 33623830 64356234 66633462 35306239 3b80d5b4fc4b50b9
│ │ │ │ -  0x00000010 33613037 39353836 30646539 63633039 3a0795860de9cc09
│ │ │ │ -  0x00000020 39303731 36312e64 65627567 00000000 907161.debug....
│ │ │ │ -  0x00000030 716f4637                            qoF7
│ │ │ │ +  0x00000000 39626233 33623135 30343866 39663439 9bb33b15048f9f49
│ │ │ │ +  0x00000010 31386630 63636233 65333961 32636265 18f0ccb3e39a2cbe
│ │ │ │ +  0x00000020 64383963 39392e64 65627567 00000000 d89c99.debug....
│ │ │ │ +  0x00000030 7d310528                            }1.(
│ │ ├── ./usr/bin/depthOfPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 616fefa62001314c75db162505a624e4bfea4175
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: b23f726ca625eb98bad53fa6c2574bd56bfe92b5
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -73,15 +73,15 @@
│ │ │ │  G(H9G rfUSH
│ │ │ │  []A\A]A^
│ │ │ │  (hidden H
│ │ │ │  []A\A]A^A_
│ │ │ │  []A\A]A^A_
│ │ │ │  []A\A]A^A_
│ │ │ │  void intervalList<iNum, iVal>::computeDepth(intervalDepthRegions<iNum, iVal>*, uint32) [with iNum = long unsigned int; iVal = int; uint32 = unsigned int]
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libutil/intervalList.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libutil/intervalList.H
│ │ │ │  id[0].open == true
│ │ │ │  _listLen > 0
│ │ │ │  _listLen <= _listMax
│ │ │ │  Unknown arg '%s'
│ │ │ │  %u	%u	%.2f	%.2f	%.2f	%.2f	%.2f	%.2f	%.2f	%.2f	%.2f
│ │ │ │  sim4begin
│ │ │ │  ##gff-version
│ │ │ │ @@ -102,15 +102,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -121,15 +121,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -202,15 +202,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -6fefa62001314c75db162505a624e4bfea4175.debug
│ │ │ │ +3f726ca625eb98bad53fa6c2574bd56bfe92b5.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -8,15 +8,15 @@
│ │ │ │    0x0000b050 56616c3e 2a2c2075 696e7433 3229205b Val>*, uint32) [
│ │ │ │    0x0000b060 77697468 20694e75 6d203d20 6c6f6e67 with iNum = long
│ │ │ │    0x0000b070 20756e73 69676e65 6420696e 743b2069  unsigned int; i
│ │ │ │    0x0000b080 56616c20 3d20696e 743b2075 696e7433 Val = int; uint3
│ │ │ │    0x0000b090 32203d20 756e7369 676e6564 20696e74 2 = unsigned int
│ │ │ │    0x0000b0a0 5d000000 00000000 2f627569 6c642f6b ]......./build/k
│ │ │ │    0x0000b0b0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000b0c0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000b0c0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000b0d0 2f6c6962 7574696c 2f696e74 65727661 /libutil/interva
│ │ │ │    0x0000b0e0 6c4c6973 742e4800 69645b30 5d2e6f70 lList.H.id[0].op
│ │ │ │    0x0000b0f0 656e203d 3d207472 7565005f 6c697374 en == true._list
│ │ │ │    0x0000b100 4c656e20 3e203000 5f6c6973 744c656e Len > 0._listLen
│ │ │ │    0x0000b110 203c3d20 5f6c6973 744d6178 00556e6b  <= _listMax.Unk
│ │ │ │    0x0000b120 6e6f776e 20617267 20272573 270a0000 nown arg '%s'...
│ │ │ │    0x0000b130 25750925 7509252e 32660925 2e326609 %u.%u.%.2f.%.2f.
│ │ │ │ @@ -102,15 +102,15 @@
│ │ │ │    0x0000b630 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000b640 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000b650 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000b660 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000b670 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000b680 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000b690 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000b6a0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000b6a0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000b6b0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000b6c0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000b6d0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000b6e0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000b6f0 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000b700 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000b710 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -173,15 +173,15 @@
│ │ │ │    0x0000baa0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000bab0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000bac0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000bad0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000bae0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000baf0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000bb00 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000bb10 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000bb10 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000bb20 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000bb30 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000bb40 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000bb50 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000bb60 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000bb70 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000bb80 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 36666566 61363230 30313331 34633735 6fefa62001314c75
│ │ │ │ -  0x00000010 64623136 32353035 61363234 65346266 db162505a624e4bf
│ │ │ │ -  0x00000020 65613431 37352e64 65627567 00000000 ea4175.debug....
│ │ │ │ -  0x00000030 ab478800                            .G..
│ │ │ │ +  0x00000000 33663732 36636136 32356562 39386261 3f726ca625eb98ba
│ │ │ │ +  0x00000010 64353366 61366332 35373462 64353662 d53fa6c2574bd56b
│ │ │ │ +  0x00000020 66653932 62352e64 65627567 00000000 fe92b5.debug....
│ │ │ │ +  0x00000030 ed83d02e                            ....
│ │ ├── ./usr/bin/detectChimera
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 0c0979bee45aa1d9ff8f9b02636e49c36b719de4
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 43ee65943a29eb33cecd24baa7c3620f26879886
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -108,15 +108,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -127,15 +127,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -208,15 +208,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -0979bee45aa1d9ff8f9b02636e49c36b719de4.debug
│ │ │ │ +ee65943a29eb33cecd24baa7c3620f26879886.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -92,15 +92,15 @@
│ │ │ │    0x0000b590 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000b5a0 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000b5b0 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000b5c0 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000b5d0 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000b5e0 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000b5f0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000b600 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000b600 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000b610 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000b620 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000b630 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000b640 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000b650 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000b660 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000b670 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -163,15 +163,15 @@
│ │ │ │    0x0000ba00 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000ba10 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000ba20 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000ba30 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000ba40 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000ba50 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000ba60 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000ba70 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000ba70 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000ba80 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000ba90 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000baa0 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000bab0 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000bac0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000bad0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000bae0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 30393739 62656534 35616131 64396666 0979bee45aa1d9ff
│ │ │ │ -  0x00000010 38663962 30323633 36653439 63333662 8f9b02636e49c36b
│ │ │ │ -  0x00000020 37313964 65342e64 65627567 00000000 719de4.debug....
│ │ │ │ -  0x00000030 d3ead8ec                            ....
│ │ │ │ +  0x00000000 65653635 39343361 32396562 33336365 ee65943a29eb33ce
│ │ │ │ +  0x00000010 63643234 62616137 63333632 30663236 cd24baa7c3620f26
│ │ │ │ +  0x00000020 38373938 38362e64 65627567 00000000 879886.debug....
│ │ │ │ +  0x00000030 68bd5e6d                            h.^m
│ │ ├── ./usr/bin/filterPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: bf1bd4322e95d91aa448a5433837f6cce6b76d40
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 207a368d5ccbe7b585ac7001d068db4a25ebcaed
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -122,15 +122,15 @@
│ │ │ │  Y@char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -158,15 +158,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -239,15 +239,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -1bd4322e95d91aa448a5433837f6cce6b76d40.debug
│ │ │ │ +7a368d5ccbe7b585ac7001d068db4a25ebcaed.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -163,15 +163,15 @@
│ │ │ │    0x0000ba00 202d2d00 203c2d00 202d3e00 554e4b4e  --. <-. ->.UNKN
│ │ │ │    0x0000ba10 4f574e00 6572726f 72006162 6f727465 OWN.error.aborte
│ │ │ │    0x0000ba20 6400696e 74726163 7461626c 6500756e d.intractable.un
│ │ │ │    0x0000ba30 6b6e6f77 6e007265 76657273 6500666f known.reverse.fo
│ │ │ │    0x0000ba40 72776172 6400636f 6d706c65 6d656e74 rward.complement
│ │ │ │    0x0000ba50 00000000 00000000 2f627569 6c642f6b ......../build/k
│ │ │ │    0x0000ba60 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000ba70 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000ba70 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000ba80 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000ba90 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x0000baa0 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x0000bab0 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x0000bac0 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x0000bad0 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x0000bae0 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -297,15 +297,15 @@
│ │ │ │    0x0000c260 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000c270 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000c280 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000c290 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000c2a0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000c2b0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000c2c0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000c2d0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000c2d0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000c2e0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000c2f0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000c300 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000c310 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000c320 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000c330 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000c340 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 31626434 33323265 39356439 31616134 1bd4322e95d91aa4
│ │ │ │ -  0x00000010 34386135 34333338 33376636 63636536 48a5433837f6cce6
│ │ │ │ -  0x00000020 62373664 34302e64 65627567 00000000 b76d40.debug....
│ │ │ │ -  0x00000030 c9fb19a6                            ....
│ │ │ │ +  0x00000000 37613336 38643563 63626537 62353835 7a368d5ccbe7b585
│ │ │ │ +  0x00000010 61633730 30316430 36386462 34613235 ac7001d068db4a25
│ │ │ │ +  0x00000020 65626361 65642e64 65627567 00000000 ebcaed.debug....
│ │ │ │ +  0x00000030 bf8866fe                            ..f.
│ │ ├── ./usr/bin/fixPolishesIID
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 23ccdb7f1c7cf529737598da572e8127b4fcf556
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: cd16727eb741bcb7eb5a58534900af07007cdb8e
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -188,15 +188,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -224,15 +224,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -264,15 +264,15 @@
│ │ │ │  Parent=sim4db
│ │ │ │  Parent=sim4db%u
│ │ │ │  Target=%s %u %u %c
│ │ │ │  nMatches=
│ │ │ │  nMatches=%u
│ │ │ │  intron=%s
│ │ │ │  ?seqCache::loadAllSequences()-- Failed to load iid %u.
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqFactory.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqFactory.C
│ │ │ │  seqFactory::registerFile()--  Wow!  You registered lots of files!  Now fix %s at line %d.
│ │ │ │  seqFactory::registerFile()--  Cannot determine type of file '%s'.  Tried:
│ │ │ │  seqFactory::registerFile()--         '%s'
│ │ │ │  fastaFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(part)-- ERROR2: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(full)-- ERROR1: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │ @@ -285,15 +285,15 @@
│ │ │ │  fastaFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │  fastaFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastaidx
│ │ │ │  7seqFile
│ │ │ │  9fastaFile
│ │ │ │  kmerFastaFileIdxfastaStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastaStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastaStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastaStdin.C
│ │ │ │  fastaStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastaStdin::loadNextSequence(part)-- ERROR: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaStdin::getSequenceLength()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastaStdin::getSequenceLength(uint32)
│ │ │ │  fastaStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ @@ -303,15 +303,15 @@
│ │ │ │  10fastaStdin
│ │ │ │  fastqFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(part)-- ERROR2: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(full)-- ERROR1: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence()-- ERROR: sequence is too long; must be less than 4 Gbp.
│ │ │ │  virtual bool fastqFile::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqFile.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqFile.C
│ │ │ │  (_rb->eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- open of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- magic mismatch.
│ │ │ │  fastqFile::constructIndex()-- stat mismatch.
│ │ │ │  fastqFile::constructIndex()-- ERROR3: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │ @@ -319,15 +319,15 @@
│ │ │ │  (ib.eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastqidx
│ │ │ │  REALLOC len=%u from %u to %u
│ │ │ │  9fastqFile
│ │ │ │  fastqStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastqStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqStdin.C
│ │ │ │  fastqStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastqStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastqStdin::loadNextSequence(part)-- ERROR: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  bool fastqStdin::loadNextSequence(char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │  fastqStdin::getSequence()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastqStdin::getSequenceLength(uint32)
│ │ │ │  fastqStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │ @@ -336,23 +336,23 @@
│ │ │ │  sLen == _block[block]._pos
│ │ │ │  sPos == _block[block]._pos
│ │ │ │  _isReadOnly == false
│ │ │ │  seqStore::seqStore()--  Failed to open '%s': %s
│ │ │ │  seqStore::seqStore()--  Failed to read index from '%s': %s
│ │ │ │  seqStore::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  virtual bool seqStore::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqStore.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqStore.C
│ │ │ │  _bpf->tell() == _block[block]._bpf * 2
│ │ │ │  seqStore::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  seqStore::getSequence(part)--  for iid %u; invalid bgn=%u end=%u; seqLen=%u
│ │ │ │  virtual bool seqStore::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  constructSeqStore()-- constructing seqStore '%s' from seqCache '%s' of type '%s'.
│ │ │ │   reading sequences %7.0f sequences -- %5.0f sequences/second
│ │ │ │  void bitPackedFile::putBits(uint64, uint32)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libutil/bitPackedFile.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libutil/bitPackedFile.H
│ │ │ │  constructSeqStore()--  Failed to reopen '%s' to write data: %s
│ │ │ │  constructSeqStore()--  Failed to write data to '%s': %s
│ │ │ │  constructSeqStore()-- seqStore '%s' constructed (%u sequences, %lu ACGT letters, %u ACGT blocks, %u GAP blocks).
│ │ │ │  8seqStore
│ │ │ │  kmerSeqStoreFile/XXXXXX
│ │ │ │  Couldn't open() '%s'
│ │ │ │  Couldn't fstat() '%s'
│ │ │ │ @@ -418,15 +418,15 @@
│ │ │ │  [        --]
│ │ │ │  [         -]
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -ccdb7f1c7cf529737598da572e8127b4fcf556.debug
│ │ │ │ +16727eb741bcb7eb5a58534900af07007cdb8e.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -52,15 +52,15 @@
│ │ │ │    0x00015310 25730a00 203f3f00 203d3d00 202d2d00 %s.. ??. ==. --.
│ │ │ │    0x00015320 203c2d00 202d3e00 554e4b4e 4f574e00  <-. ->.UNKNOWN.
│ │ │ │    0x00015330 6572726f 72006162 6f727465 6400696e error.aborted.in
│ │ │ │    0x00015340 74726163 7461626c 6500756e 6b6e6f77 tractable.unknow
│ │ │ │    0x00015350 6e007265 76657273 6500666f 72776172 n.reverse.forwar
│ │ │ │    0x00015360 6400636f 6d706c65 6d656e74 00000000 d.complement....
│ │ │ │    0x00015370 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00015380 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00015380 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00015390 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x000153a0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x000153b0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x000153c0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x000153d0 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x000153e0 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x000153f0 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -185,15 +185,15 @@
│ │ │ │    0x00015b60 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x00015b70 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x00015b80 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x00015b90 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x00015ba0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x00015bb0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x00015bc0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00015bd0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00015bd0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00015be0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x00015bf0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x00015c00 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x00015c10 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x00015c20 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x00015c30 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x00015c40 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ │ @@ -308,15 +308,15 @@
│ │ │ │    0x00016310 231bffff 251fffff 231bffff 311fffff #...%...#...1...
│ │ │ │    0x00016320 231bffff 3d1fffff 00000000 00005940 #...=.........Y@
│ │ │ │    0x00016330 00000000 0000f03f 73657143 61636865 .......?seqCache
│ │ │ │    0x00016340 3a3a6c6f 6164416c 6c536571 75656e63 ::loadAllSequenc
│ │ │ │    0x00016350 65732829 2d2d2046 61696c65 6420746f es()-- Failed to
│ │ │ │    0x00016360 206c6f61 64206969 64202575 2e0a0000  load iid %u....
│ │ │ │    0x00016370 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00016380 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00016380 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00016390 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x000163a0 73657146 6163746f 72792e43 00000000 seqFactory.C....
│ │ │ │    0x000163b0 73657146 6163746f 72793a3a 72656769 seqFactory::regi
│ │ │ │    0x000163c0 73746572 46696c65 28292d2d 2020576f sterFile()--  Wo
│ │ │ │    0x000163d0 77212020 596f7520 72656769 73746572 w!  You register
│ │ │ │    0x000163e0 6564206c 6f747320 6f662066 696c6573 ed lots of files
│ │ │ │    0x000163f0 2120204e 6f772066 69782025 73206174 !  Now fix %s at
│ │ │ │ @@ -397,15 +397,15 @@
│ │ │ │    0x000168a0 28292d2d 20455252 4f522120 20557365 ()-- ERROR!  Use
│ │ │ │    0x000168b0 6420666f 72207261 6e646f6d 20616363 d for random acc
│ │ │ │    0x000168c0 6573732e 0a000000 76697274 75616c20 ess.....virtual 
│ │ │ │    0x000168d0 75696e74 33322066 61737461 53746469 uint32 fastaStdi
│ │ │ │    0x000168e0 6e3a3a66 696e6428 636f6e73 74206368 n::find(const ch
│ │ │ │    0x000168f0 61722a29 00000000 2f627569 6c642f6b ar*)..../build/k
│ │ │ │    0x00016900 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00016910 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00016910 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00016920 2f6c6962 7365712f 66617374 61537464 /libseq/fastaStd
│ │ │ │    0x00016930 696e2e43 00000000 66617374 61537464 in.C....fastaStd
│ │ │ │    0x00016940 696e3a3a 67657453 65717565 6e636528 in::getSequence(
│ │ │ │    0x00016950 70617274 292d2d20 4552524f 52212020 part)-- ERROR!  
│ │ │ │    0x00016960 55736564 20666f72 2072616e 646f6d20 Used for random 
│ │ │ │    0x00016970 61636365 73732e0a 00000000 00000000 access..........
│ │ │ │    0x00016980 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │ @@ -476,15 +476,15 @@
│ │ │ │    0x00016d90 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │    0x00016da0 74714669 6c653a3a 67657453 65717565 tqFile::getSeque
│ │ │ │    0x00016db0 6e636528 75696e74 33322c20 63686172 nce(uint32, char
│ │ │ │    0x00016dc0 2a262c20 75696e74 3332262c 2075696e *&, uint32&, uin
│ │ │ │    0x00016dd0 74333226 2c206368 61722a26 2c207569 t32&, char*&, ui
│ │ │ │    0x00016de0 6e743332 262c2075 696e7433 32262900 nt32&, uint32&).
│ │ │ │    0x00016df0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00016e00 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00016e00 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00016e10 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00016e20 66617374 7146696c 652e4300 00000000 fastqFile.C.....
│ │ │ │    0x00016e30 285f7262 2d3e656f 66282920 3d3d2074 (_rb->eof() == t
│ │ │ │    0x00016e40 72756529 207c7c20 2878203d 3d20272b rue) || (x == '+
│ │ │ │    0x00016e50 27290000 00000000 66617374 7146696c ')......fastqFil
│ │ │ │    0x00016e60 653a3a63 6f6e7374 72756374 496e6465 e::constructInde
│ │ │ │    0x00016e70 7828292d 2d207374 6174206f 66206669 x()-- stat of fi
│ │ │ │ @@ -529,15 +529,15 @@
│ │ │ │    0x000170e0 696e3a3a 66696e64 28292d2d 20455252 in::find()-- ERR
│ │ │ │    0x000170f0 4f522120 20557365 6420666f 72207261 OR!  Used for ra
│ │ │ │    0x00017100 6e646f6d 20616363 6573732e 0a000000 ndom access.....
│ │ │ │    0x00017110 76697274 75616c20 75696e74 33322066 virtual uint32 f
│ │ │ │    0x00017120 61737471 53746469 6e3a3a66 696e6428 astqStdin::find(
│ │ │ │    0x00017130 636f6e73 74206368 61722a29 00000000 const char*)....
│ │ │ │    0x00017140 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00017150 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00017150 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00017160 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00017170 66617374 71537464 696e2e43 00000000 fastqStdin.C....
│ │ │ │    0x00017180 66617374 71537464 696e3a3a 67657453 fastqStdin::getS
│ │ │ │    0x00017190 65717565 6e636528 70617274 292d2d20 equence(part)-- 
│ │ │ │    0x000171a0 4552524f 52212020 55736564 20666f72 ERROR!  Used for
│ │ │ │    0x000171b0 2072616e 646f6d20 61636365 73732e0a  random access..
│ │ │ │    0x000171c0 00000000 00000000 76697274 75616c20 ........virtual 
│ │ │ │ @@ -601,15 +601,15 @@
│ │ │ │    0x00017560 626f6f6c 20736571 53746f72 653a3a67 bool seqStore::g
│ │ │ │    0x00017570 65745365 7175656e 63652875 696e7433 etSequence(uint3
│ │ │ │    0x00017580 322c2063 6861722a 262c2075 696e7433 2, char*&, uint3
│ │ │ │    0x00017590 32262c20 75696e74 3332262c 20636861 2&, uint32&, cha
│ │ │ │    0x000175a0 722a262c 2075696e 74333226 2c207569 r*&, uint32&, ui
│ │ │ │    0x000175b0 6e743332 26290000 2f627569 6c642f6b nt32&)../build/k
│ │ │ │    0x000175c0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x000175d0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x000175d0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x000175e0 2f6c6962 7365712f 73657153 746f7265 /libseq/seqStore
│ │ │ │    0x000175f0 2e430000 00000000 5f627066 2d3e7465 .C......_bpf->te
│ │ │ │    0x00017600 6c6c2829 203d3d20 5f626c6f 636b5b62 ll() == _block[b
│ │ │ │    0x00017610 6c6f636b 5d2e5f62 7066202a 20320000 lock]._bpf * 2..
│ │ │ │    0x00017620 73657153 746f7265 3a3a6765 74536571 seqStore::getSeq
│ │ │ │    0x00017630 75656e63 65287061 7274292d 2d202069 uence(part)--  i
│ │ │ │    0x00017640 69642025 75206d6f 72652074 68616e20 id %u more than 
│ │ │ │ @@ -634,15 +634,15 @@
│ │ │ │    0x00017770 20736571 75656e63 6573202d 2d202535  sequences -- %5
│ │ │ │    0x00017780 2e306620 73657175 656e6365 732f7365 .0f sequences/se
│ │ │ │    0x00017790 636f6e64 0d000000 766f6964 20626974 cond....void bit
│ │ │ │    0x000177a0 5061636b 65644669 6c653a3a 70757442 PackedFile::putB
│ │ │ │    0x000177b0 69747328 75696e74 36342c20 75696e74 its(uint64, uint
│ │ │ │    0x000177c0 33322900 00000000 2f627569 6c642f6b 32)...../build/k
│ │ │ │    0x000177d0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x000177e0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x000177e0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x000177f0 2f6c6962 7574696c 2f626974 5061636b /libutil/bitPack
│ │ │ │    0x00017800 65644669 6c652e48 00000000 00000000 edFile.H........
│ │ │ │    0x00017810 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ │    0x00017820 6528292d 2d202046 61696c65 6420746f e()--  Failed to
│ │ │ │    0x00017830 2072656f 70656e20 27257327 20746f20  reopen '%s' to 
│ │ │ │    0x00017840 77726974 65206461 74613a20 25730a00 write data: %s..
│ │ │ │    0x00017850 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 63636462 37663163 37636635 32393733 ccdb7f1c7cf52973
│ │ │ │ -  0x00000010 37353938 64613537 32653831 32376234 7598da572e8127b4
│ │ │ │ -  0x00000020 66636635 35362e64 65627567 00000000 fcf556.debug....
│ │ │ │ -  0x00000030 276ef63d                            'n.=
│ │ │ │ +  0x00000000 31363732 37656237 34316263 62376562 16727eb741bcb7eb
│ │ │ │ +  0x00000010 35613538 35333439 30306166 30373030 5a58534900af0700
│ │ │ │ +  0x00000020 37636462 38652e64 65627567 00000000 7cdb8e.debug....
│ │ │ │ +  0x00000030 5a4c77ec                            ZLw.
│ │ ├── ./usr/bin/headPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: b352f76611889179d56b30202fc82266541db9c7
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 9ce3d39ad16c8842b516da8b37495b0d232184fa
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -78,15 +78,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -114,15 +114,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -195,15 +195,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -52f76611889179d56b30202fc82266541db9c7.debug
│ │ │ │ +e3d39ad16c8842b516da8b37495b0d232184fa.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -19,15 +19,15 @@
│ │ │ │    0x0000a100 00202d2d 00203c2d 00202d3e 00554e4b . --. <-. ->.UNK
│ │ │ │    0x0000a110 4e4f574e 00657272 6f720061 626f7274 NOWN.error.abort
│ │ │ │    0x0000a120 65640069 6e747261 63746162 6c650075 ed.intractable.u
│ │ │ │    0x0000a130 6e6b6e6f 776e0072 65766572 73650066 nknown.reverse.f
│ │ │ │    0x0000a140 6f727761 72640063 6f6d706c 656d656e orward.complemen
│ │ │ │    0x0000a150 74000000 00000000 2f627569 6c642f6b t......./build/k
│ │ │ │    0x0000a160 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000a170 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000a170 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000a180 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000a190 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x0000a1a0 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x0000a1b0 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x0000a1c0 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x0000a1d0 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x0000a1e0 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -153,15 +153,15 @@
│ │ │ │    0x0000a960 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000a970 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000a980 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000a990 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000a9a0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000a9b0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000a9c0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000a9d0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000a9d0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000a9e0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000a9f0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000aa00 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000aa10 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000aa20 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000aa30 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000aa40 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 35326637 36363131 38383931 37396435 52f76611889179d5
│ │ │ │ -  0x00000010 36623330 32303266 63383232 36363534 6b30202fc8226654
│ │ │ │ -  0x00000020 31646239 63372e64 65627567 00000000 1db9c7.debug....
│ │ │ │ -  0x00000030 f10d19f0                            ....
│ │ │ │ +  0x00000000 65336433 39616431 36633838 34326235 e3d39ad16c8842b5
│ │ │ │ +  0x00000010 31366461 38623337 34393562 30643233 16da8b37495b0d23
│ │ │ │ +  0x00000020 32313834 66612e64 65627567 00000000 2184fa.debug....
│ │ │ │ +  0x00000030 a79bdeef                            ....
│ │ ├── ./usr/bin/mappedCoverage
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 7a9c468b7b342f9bac10a01f1ecfed448779a772
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: c228a70427151a74c3de925178ef70febe24f6ca
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -200,15 +200,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -219,15 +219,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -259,15 +259,15 @@
│ │ │ │  Parent=sim4db
│ │ │ │  Parent=sim4db%u
│ │ │ │  Target=%s %u %u %c
│ │ │ │  nMatches=
│ │ │ │  nMatches=%u
│ │ │ │  intron=%s
│ │ │ │  ?seqCache::loadAllSequences()-- Failed to load iid %u.
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqFactory.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqFactory.C
│ │ │ │  seqFactory::registerFile()--  Wow!  You registered lots of files!  Now fix %s at line %d.
│ │ │ │  seqFactory::registerFile()--  Cannot determine type of file '%s'.  Tried:
│ │ │ │  seqFactory::registerFile()--         '%s'
│ │ │ │  fastaFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(part)-- ERROR2: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(full)-- ERROR1: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │ @@ -280,15 +280,15 @@
│ │ │ │  fastaFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │  fastaFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastaidx
│ │ │ │  7seqFile
│ │ │ │  9fastaFile
│ │ │ │  kmerFastaFileIdxfastaStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastaStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastaStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastaStdin.C
│ │ │ │  fastaStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastaStdin::loadNextSequence(part)-- ERROR: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaStdin::getSequenceLength()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastaStdin::getSequenceLength(uint32)
│ │ │ │  fastaStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ @@ -298,15 +298,15 @@
│ │ │ │  10fastaStdin
│ │ │ │  fastqFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(part)-- ERROR2: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(full)-- ERROR1: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence()-- ERROR: sequence is too long; must be less than 4 Gbp.
│ │ │ │  virtual bool fastqFile::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqFile.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqFile.C
│ │ │ │  (_rb->eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- open of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- magic mismatch.
│ │ │ │  fastqFile::constructIndex()-- stat mismatch.
│ │ │ │  fastqFile::constructIndex()-- ERROR3: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │ @@ -314,15 +314,15 @@
│ │ │ │  (ib.eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastqidx
│ │ │ │  REALLOC len=%u from %u to %u
│ │ │ │  9fastqFile
│ │ │ │  fastqStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastqStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqStdin.C
│ │ │ │  fastqStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastqStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastqStdin::loadNextSequence(part)-- ERROR: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  bool fastqStdin::loadNextSequence(char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │  fastqStdin::getSequence()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastqStdin::getSequenceLength(uint32)
│ │ │ │  fastqStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │ @@ -331,23 +331,23 @@
│ │ │ │  sLen == _block[block]._pos
│ │ │ │  sPos == _block[block]._pos
│ │ │ │  _isReadOnly == false
│ │ │ │  seqStore::seqStore()--  Failed to open '%s': %s
│ │ │ │  seqStore::seqStore()--  Failed to read index from '%s': %s
│ │ │ │  seqStore::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  virtual bool seqStore::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqStore.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqStore.C
│ │ │ │  _bpf->tell() == _block[block]._bpf * 2
│ │ │ │  seqStore::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  seqStore::getSequence(part)--  for iid %u; invalid bgn=%u end=%u; seqLen=%u
│ │ │ │  virtual bool seqStore::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  constructSeqStore()-- constructing seqStore '%s' from seqCache '%s' of type '%s'.
│ │ │ │   reading sequences %7.0f sequences -- %5.0f sequences/second
│ │ │ │  void bitPackedFile::putBits(uint64, uint32)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libutil/bitPackedFile.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libutil/bitPackedFile.H
│ │ │ │  constructSeqStore()--  Failed to reopen '%s' to write data: %s
│ │ │ │  constructSeqStore()--  Failed to write data to '%s': %s
│ │ │ │  constructSeqStore()-- seqStore '%s' constructed (%u sequences, %lu ACGT letters, %u ACGT blocks, %u GAP blocks).
│ │ │ │  8seqStore
│ │ │ │  kmerSeqStoreFile/XXXXXX
│ │ │ │  Couldn't open() '%s'
│ │ │ │  Couldn't fstat() '%s'
│ │ │ │ @@ -413,15 +413,15 @@
│ │ │ │  [        --]
│ │ │ │  [         -]
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -9c468b7b342f9bac10a01f1ecfed448779a772.debug
│ │ │ │ +28a70427151a74c3de925178ef70febe24f6ca.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -156,15 +156,15 @@
│ │ │ │    0x00016990 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x000169a0 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x000169b0 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x000169c0 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x000169d0 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x000169e0 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x000169f0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00016a00 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00016a00 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00016a10 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x00016a20 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x00016a30 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x00016a40 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x00016a50 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x00016a60 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x00016a70 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -227,15 +227,15 @@
│ │ │ │    0x00016e00 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x00016e10 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x00016e20 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x00016e30 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x00016e40 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x00016e50 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x00016e60 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00016e70 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00016e70 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00016e80 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x00016e90 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x00016ea0 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x00016eb0 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x00016ec0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x00016ed0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x00016ee0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ │ @@ -350,15 +350,15 @@
│ │ │ │    0x000175b0 a313ffff a517ffff a313ffff b117ffff ................
│ │ │ │    0x000175c0 a313ffff bd17ffff 00000000 00005940 ..............Y@
│ │ │ │    0x000175d0 00000000 0000f03f 73657143 61636865 .......?seqCache
│ │ │ │    0x000175e0 3a3a6c6f 6164416c 6c536571 75656e63 ::loadAllSequenc
│ │ │ │    0x000175f0 65732829 2d2d2046 61696c65 6420746f es()-- Failed to
│ │ │ │    0x00017600 206c6f61 64206969 64202575 2e0a0000  load iid %u....
│ │ │ │    0x00017610 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00017620 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00017620 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00017630 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00017640 73657146 6163746f 72792e43 00000000 seqFactory.C....
│ │ │ │    0x00017650 73657146 6163746f 72793a3a 72656769 seqFactory::regi
│ │ │ │    0x00017660 73746572 46696c65 28292d2d 2020576f sterFile()--  Wo
│ │ │ │    0x00017670 77212020 596f7520 72656769 73746572 w!  You register
│ │ │ │    0x00017680 6564206c 6f747320 6f662066 696c6573 ed lots of files
│ │ │ │    0x00017690 2120204e 6f772066 69782025 73206174 !  Now fix %s at
│ │ │ │ @@ -439,15 +439,15 @@
│ │ │ │    0x00017b40 28292d2d 20455252 4f522120 20557365 ()-- ERROR!  Use
│ │ │ │    0x00017b50 6420666f 72207261 6e646f6d 20616363 d for random acc
│ │ │ │    0x00017b60 6573732e 0a000000 76697274 75616c20 ess.....virtual 
│ │ │ │    0x00017b70 75696e74 33322066 61737461 53746469 uint32 fastaStdi
│ │ │ │    0x00017b80 6e3a3a66 696e6428 636f6e73 74206368 n::find(const ch
│ │ │ │    0x00017b90 61722a29 00000000 2f627569 6c642f6b ar*)..../build/k
│ │ │ │    0x00017ba0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00017bb0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00017bb0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00017bc0 2f6c6962 7365712f 66617374 61537464 /libseq/fastaStd
│ │ │ │    0x00017bd0 696e2e43 00000000 66617374 61537464 in.C....fastaStd
│ │ │ │    0x00017be0 696e3a3a 67657453 65717565 6e636528 in::getSequence(
│ │ │ │    0x00017bf0 70617274 292d2d20 4552524f 52212020 part)-- ERROR!  
│ │ │ │    0x00017c00 55736564 20666f72 2072616e 646f6d20 Used for random 
│ │ │ │    0x00017c10 61636365 73732e0a 00000000 00000000 access..........
│ │ │ │    0x00017c20 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │ @@ -518,15 +518,15 @@
│ │ │ │    0x00018030 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │    0x00018040 74714669 6c653a3a 67657453 65717565 tqFile::getSeque
│ │ │ │    0x00018050 6e636528 75696e74 33322c20 63686172 nce(uint32, char
│ │ │ │    0x00018060 2a262c20 75696e74 3332262c 2075696e *&, uint32&, uin
│ │ │ │    0x00018070 74333226 2c206368 61722a26 2c207569 t32&, char*&, ui
│ │ │ │    0x00018080 6e743332 262c2075 696e7433 32262900 nt32&, uint32&).
│ │ │ │    0x00018090 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000180a0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000180a0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000180b0 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x000180c0 66617374 7146696c 652e4300 00000000 fastqFile.C.....
│ │ │ │    0x000180d0 285f7262 2d3e656f 66282920 3d3d2074 (_rb->eof() == t
│ │ │ │    0x000180e0 72756529 207c7c20 2878203d 3d20272b rue) || (x == '+
│ │ │ │    0x000180f0 27290000 00000000 66617374 7146696c ')......fastqFil
│ │ │ │    0x00018100 653a3a63 6f6e7374 72756374 496e6465 e::constructInde
│ │ │ │    0x00018110 7828292d 2d207374 6174206f 66206669 x()-- stat of fi
│ │ │ │ @@ -571,15 +571,15 @@
│ │ │ │    0x00018380 696e3a3a 66696e64 28292d2d 20455252 in::find()-- ERR
│ │ │ │    0x00018390 4f522120 20557365 6420666f 72207261 OR!  Used for ra
│ │ │ │    0x000183a0 6e646f6d 20616363 6573732e 0a000000 ndom access.....
│ │ │ │    0x000183b0 76697274 75616c20 75696e74 33322066 virtual uint32 f
│ │ │ │    0x000183c0 61737471 53746469 6e3a3a66 696e6428 astqStdin::find(
│ │ │ │    0x000183d0 636f6e73 74206368 61722a29 00000000 const char*)....
│ │ │ │    0x000183e0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000183f0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000183f0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00018400 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00018410 66617374 71537464 696e2e43 00000000 fastqStdin.C....
│ │ │ │    0x00018420 66617374 71537464 696e3a3a 67657453 fastqStdin::getS
│ │ │ │    0x00018430 65717565 6e636528 70617274 292d2d20 equence(part)-- 
│ │ │ │    0x00018440 4552524f 52212020 55736564 20666f72 ERROR!  Used for
│ │ │ │    0x00018450 2072616e 646f6d20 61636365 73732e0a  random access..
│ │ │ │    0x00018460 00000000 00000000 76697274 75616c20 ........virtual 
│ │ │ │ @@ -643,15 +643,15 @@
│ │ │ │    0x00018800 626f6f6c 20736571 53746f72 653a3a67 bool seqStore::g
│ │ │ │    0x00018810 65745365 7175656e 63652875 696e7433 etSequence(uint3
│ │ │ │    0x00018820 322c2063 6861722a 262c2075 696e7433 2, char*&, uint3
│ │ │ │    0x00018830 32262c20 75696e74 3332262c 20636861 2&, uint32&, cha
│ │ │ │    0x00018840 722a262c 2075696e 74333226 2c207569 r*&, uint32&, ui
│ │ │ │    0x00018850 6e743332 26290000 2f627569 6c642f6b nt32&)../build/k
│ │ │ │    0x00018860 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00018870 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00018870 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00018880 2f6c6962 7365712f 73657153 746f7265 /libseq/seqStore
│ │ │ │    0x00018890 2e430000 00000000 5f627066 2d3e7465 .C......_bpf->te
│ │ │ │    0x000188a0 6c6c2829 203d3d20 5f626c6f 636b5b62 ll() == _block[b
│ │ │ │    0x000188b0 6c6f636b 5d2e5f62 7066202a 20320000 lock]._bpf * 2..
│ │ │ │    0x000188c0 73657153 746f7265 3a3a6765 74536571 seqStore::getSeq
│ │ │ │    0x000188d0 75656e63 65287061 7274292d 2d202069 uence(part)--  i
│ │ │ │    0x000188e0 69642025 75206d6f 72652074 68616e20 id %u more than 
│ │ │ │ @@ -676,15 +676,15 @@
│ │ │ │    0x00018a10 20736571 75656e63 6573202d 2d202535  sequences -- %5
│ │ │ │    0x00018a20 2e306620 73657175 656e6365 732f7365 .0f sequences/se
│ │ │ │    0x00018a30 636f6e64 0d000000 766f6964 20626974 cond....void bit
│ │ │ │    0x00018a40 5061636b 65644669 6c653a3a 70757442 PackedFile::putB
│ │ │ │    0x00018a50 69747328 75696e74 36342c20 75696e74 its(uint64, uint
│ │ │ │    0x00018a60 33322900 00000000 2f627569 6c642f6b 32)...../build/k
│ │ │ │    0x00018a70 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00018a80 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00018a80 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00018a90 2f6c6962 7574696c 2f626974 5061636b /libutil/bitPack
│ │ │ │    0x00018aa0 65644669 6c652e48 00000000 00000000 edFile.H........
│ │ │ │    0x00018ab0 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ │    0x00018ac0 6528292d 2d202046 61696c65 6420746f e()--  Failed to
│ │ │ │    0x00018ad0 2072656f 70656e20 27257327 20746f20  reopen '%s' to 
│ │ │ │    0x00018ae0 77726974 65206461 74613a20 25730a00 write data: %s..
│ │ │ │    0x00018af0 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 39633436 38623762 33343266 39626163 9c468b7b342f9bac
│ │ │ │ -  0x00000010 31306130 31663165 63666564 34343837 10a01f1ecfed4487
│ │ │ │ -  0x00000020 37396137 37322e64 65627567 00000000 79a772.debug....
│ │ │ │ -  0x00000030 5e229bd5                            ^"..
│ │ │ │ +  0x00000000 32386137 30343237 31353161 37346333 28a70427151a74c3
│ │ │ │ +  0x00000010 64653932 35313738 65663730 66656265 de925178ef70febe
│ │ │ │ +  0x00000020 32346636 63612e64 65627567 00000000 24f6ca.debug....
│ │ │ │ +  0x00000030 9e2eb658                            ...X
│ │ ├── ./usr/bin/mergePolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 289f8c1032b960d590a1d5f529a9e37d84da775c
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: dd59f5485f1d867cd1d941f58ce3d479086e1035
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -158,15 +158,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -194,15 +194,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -234,15 +234,15 @@
│ │ │ │  Parent=sim4db
│ │ │ │  Parent=sim4db%u
│ │ │ │  Target=%s %u %u %c
│ │ │ │  nMatches=
│ │ │ │  nMatches=%u
│ │ │ │  intron=%s
│ │ │ │  ?seqCache::loadAllSequences()-- Failed to load iid %u.
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqFactory.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqFactory.C
│ │ │ │  seqFactory::registerFile()--  Wow!  You registered lots of files!  Now fix %s at line %d.
│ │ │ │  seqFactory::registerFile()--  Cannot determine type of file '%s'.  Tried:
│ │ │ │  seqFactory::registerFile()--         '%s'
│ │ │ │  fastaFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(part)-- ERROR2: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(full)-- ERROR1: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │ @@ -255,15 +255,15 @@
│ │ │ │  fastaFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │  fastaFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastaidx
│ │ │ │  7seqFile
│ │ │ │  9fastaFile
│ │ │ │  kmerFastaFileIdxfastaStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastaStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastaStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastaStdin.C
│ │ │ │  fastaStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastaStdin::loadNextSequence(part)-- ERROR: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaStdin::getSequenceLength()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastaStdin::getSequenceLength(uint32)
│ │ │ │  fastaStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ @@ -273,15 +273,15 @@
│ │ │ │  10fastaStdin
│ │ │ │  fastqFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(part)-- ERROR2: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(full)-- ERROR1: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence()-- ERROR: sequence is too long; must be less than 4 Gbp.
│ │ │ │  virtual bool fastqFile::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqFile.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqFile.C
│ │ │ │  (_rb->eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- open of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- magic mismatch.
│ │ │ │  fastqFile::constructIndex()-- stat mismatch.
│ │ │ │  fastqFile::constructIndex()-- ERROR3: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │ @@ -289,15 +289,15 @@
│ │ │ │  (ib.eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastqidx
│ │ │ │  REALLOC len=%u from %u to %u
│ │ │ │  9fastqFile
│ │ │ │  fastqStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastqStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqStdin.C
│ │ │ │  fastqStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastqStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastqStdin::loadNextSequence(part)-- ERROR: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  bool fastqStdin::loadNextSequence(char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │  fastqStdin::getSequence()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastqStdin::getSequenceLength(uint32)
│ │ │ │  fastqStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │ @@ -306,23 +306,23 @@
│ │ │ │  sLen == _block[block]._pos
│ │ │ │  sPos == _block[block]._pos
│ │ │ │  _isReadOnly == false
│ │ │ │  seqStore::seqStore()--  Failed to open '%s': %s
│ │ │ │  seqStore::seqStore()--  Failed to read index from '%s': %s
│ │ │ │  seqStore::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  virtual bool seqStore::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqStore.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqStore.C
│ │ │ │  _bpf->tell() == _block[block]._bpf * 2
│ │ │ │  seqStore::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  seqStore::getSequence(part)--  for iid %u; invalid bgn=%u end=%u; seqLen=%u
│ │ │ │  virtual bool seqStore::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  constructSeqStore()-- constructing seqStore '%s' from seqCache '%s' of type '%s'.
│ │ │ │   reading sequences %7.0f sequences -- %5.0f sequences/second
│ │ │ │  void bitPackedFile::putBits(uint64, uint32)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libutil/bitPackedFile.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libutil/bitPackedFile.H
│ │ │ │  constructSeqStore()--  Failed to reopen '%s' to write data: %s
│ │ │ │  constructSeqStore()--  Failed to write data to '%s': %s
│ │ │ │  constructSeqStore()-- seqStore '%s' constructed (%u sequences, %lu ACGT letters, %u ACGT blocks, %u GAP blocks).
│ │ │ │  8seqStore
│ │ │ │  kmerSeqStoreFile/XXXXXX
│ │ │ │  Couldn't open() '%s'
│ │ │ │  Couldn't fstat() '%s'
│ │ │ │ @@ -388,15 +388,15 @@
│ │ │ │  [        --]
│ │ │ │  [         -]
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -9f8c1032b960d590a1d5f529a9e37d84da775c.debug
│ │ │ │ +59f5485f1d867cd1d941f58ce3d479086e1035.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -27,15 +27,15 @@
│ │ │ │    0x00015180 3d00202d 2d00203c 2d00202d 3e00554e =. --. <-. ->.UN
│ │ │ │    0x00015190 4b4e4f57 4e006572 726f7200 61626f72 KNOWN.error.abor
│ │ │ │    0x000151a0 74656400 696e7472 61637461 626c6500 ted.intractable.
│ │ │ │    0x000151b0 756e6b6e 6f776e00 72657665 72736500 unknown.reverse.
│ │ │ │    0x000151c0 666f7277 61726400 636f6d70 6c656d65 forward.compleme
│ │ │ │    0x000151d0 6e740000 00000000 2f627569 6c642f6b nt....../build/k
│ │ │ │    0x000151e0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x000151f0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x000151f0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00015200 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x00015210 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x00015220 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x00015230 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x00015240 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x00015250 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x00015260 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -161,15 +161,15 @@
│ │ │ │    0x000159e0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x000159f0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x00015a00 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x00015a10 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x00015a20 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x00015a30 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x00015a40 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00015a50 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00015a50 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00015a60 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x00015a70 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x00015a80 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x00015a90 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x00015aa0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x00015ab0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x00015ac0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ │ @@ -284,15 +284,15 @@
│ │ │ │    0x00016190 731effff 7522ffff 731effff 8122ffff s...u"..s...."..
│ │ │ │    0x000161a0 731effff 8d22ffff 00000000 00005940 s...."........Y@
│ │ │ │    0x000161b0 00000000 0000f03f 73657143 61636865 .......?seqCache
│ │ │ │    0x000161c0 3a3a6c6f 6164416c 6c536571 75656e63 ::loadAllSequenc
│ │ │ │    0x000161d0 65732829 2d2d2046 61696c65 6420746f es()-- Failed to
│ │ │ │    0x000161e0 206c6f61 64206969 64202575 2e0a0000  load iid %u....
│ │ │ │    0x000161f0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00016200 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00016200 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00016210 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00016220 73657146 6163746f 72792e43 00000000 seqFactory.C....
│ │ │ │    0x00016230 73657146 6163746f 72793a3a 72656769 seqFactory::regi
│ │ │ │    0x00016240 73746572 46696c65 28292d2d 2020576f sterFile()--  Wo
│ │ │ │    0x00016250 77212020 596f7520 72656769 73746572 w!  You register
│ │ │ │    0x00016260 6564206c 6f747320 6f662066 696c6573 ed lots of files
│ │ │ │    0x00016270 2120204e 6f772066 69782025 73206174 !  Now fix %s at
│ │ │ │ @@ -373,15 +373,15 @@
│ │ │ │    0x00016720 28292d2d 20455252 4f522120 20557365 ()-- ERROR!  Use
│ │ │ │    0x00016730 6420666f 72207261 6e646f6d 20616363 d for random acc
│ │ │ │    0x00016740 6573732e 0a000000 76697274 75616c20 ess.....virtual 
│ │ │ │    0x00016750 75696e74 33322066 61737461 53746469 uint32 fastaStdi
│ │ │ │    0x00016760 6e3a3a66 696e6428 636f6e73 74206368 n::find(const ch
│ │ │ │    0x00016770 61722a29 00000000 2f627569 6c642f6b ar*)..../build/k
│ │ │ │    0x00016780 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00016790 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00016790 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x000167a0 2f6c6962 7365712f 66617374 61537464 /libseq/fastaStd
│ │ │ │    0x000167b0 696e2e43 00000000 66617374 61537464 in.C....fastaStd
│ │ │ │    0x000167c0 696e3a3a 67657453 65717565 6e636528 in::getSequence(
│ │ │ │    0x000167d0 70617274 292d2d20 4552524f 52212020 part)-- ERROR!  
│ │ │ │    0x000167e0 55736564 20666f72 2072616e 646f6d20 Used for random 
│ │ │ │    0x000167f0 61636365 73732e0a 00000000 00000000 access..........
│ │ │ │    0x00016800 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │ @@ -452,15 +452,15 @@
│ │ │ │    0x00016c10 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │    0x00016c20 74714669 6c653a3a 67657453 65717565 tqFile::getSeque
│ │ │ │    0x00016c30 6e636528 75696e74 33322c20 63686172 nce(uint32, char
│ │ │ │    0x00016c40 2a262c20 75696e74 3332262c 2075696e *&, uint32&, uin
│ │ │ │    0x00016c50 74333226 2c206368 61722a26 2c207569 t32&, char*&, ui
│ │ │ │    0x00016c60 6e743332 262c2075 696e7433 32262900 nt32&, uint32&).
│ │ │ │    0x00016c70 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00016c80 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00016c80 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00016c90 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00016ca0 66617374 7146696c 652e4300 00000000 fastqFile.C.....
│ │ │ │    0x00016cb0 285f7262 2d3e656f 66282920 3d3d2074 (_rb->eof() == t
│ │ │ │    0x00016cc0 72756529 207c7c20 2878203d 3d20272b rue) || (x == '+
│ │ │ │    0x00016cd0 27290000 00000000 66617374 7146696c ')......fastqFil
│ │ │ │    0x00016ce0 653a3a63 6f6e7374 72756374 496e6465 e::constructInde
│ │ │ │    0x00016cf0 7828292d 2d207374 6174206f 66206669 x()-- stat of fi
│ │ │ │ @@ -505,15 +505,15 @@
│ │ │ │    0x00016f60 696e3a3a 66696e64 28292d2d 20455252 in::find()-- ERR
│ │ │ │    0x00016f70 4f522120 20557365 6420666f 72207261 OR!  Used for ra
│ │ │ │    0x00016f80 6e646f6d 20616363 6573732e 0a000000 ndom access.....
│ │ │ │    0x00016f90 76697274 75616c20 75696e74 33322066 virtual uint32 f
│ │ │ │    0x00016fa0 61737471 53746469 6e3a3a66 696e6428 astqStdin::find(
│ │ │ │    0x00016fb0 636f6e73 74206368 61722a29 00000000 const char*)....
│ │ │ │    0x00016fc0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00016fd0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00016fd0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00016fe0 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00016ff0 66617374 71537464 696e2e43 00000000 fastqStdin.C....
│ │ │ │    0x00017000 66617374 71537464 696e3a3a 67657453 fastqStdin::getS
│ │ │ │    0x00017010 65717565 6e636528 70617274 292d2d20 equence(part)-- 
│ │ │ │    0x00017020 4552524f 52212020 55736564 20666f72 ERROR!  Used for
│ │ │ │    0x00017030 2072616e 646f6d20 61636365 73732e0a  random access..
│ │ │ │    0x00017040 00000000 00000000 76697274 75616c20 ........virtual 
│ │ │ │ @@ -577,15 +577,15 @@
│ │ │ │    0x000173e0 626f6f6c 20736571 53746f72 653a3a67 bool seqStore::g
│ │ │ │    0x000173f0 65745365 7175656e 63652875 696e7433 etSequence(uint3
│ │ │ │    0x00017400 322c2063 6861722a 262c2075 696e7433 2, char*&, uint3
│ │ │ │    0x00017410 32262c20 75696e74 3332262c 20636861 2&, uint32&, cha
│ │ │ │    0x00017420 722a262c 2075696e 74333226 2c207569 r*&, uint32&, ui
│ │ │ │    0x00017430 6e743332 26290000 2f627569 6c642f6b nt32&)../build/k
│ │ │ │    0x00017440 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00017450 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00017450 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00017460 2f6c6962 7365712f 73657153 746f7265 /libseq/seqStore
│ │ │ │    0x00017470 2e430000 00000000 5f627066 2d3e7465 .C......_bpf->te
│ │ │ │    0x00017480 6c6c2829 203d3d20 5f626c6f 636b5b62 ll() == _block[b
│ │ │ │    0x00017490 6c6f636b 5d2e5f62 7066202a 20320000 lock]._bpf * 2..
│ │ │ │    0x000174a0 73657153 746f7265 3a3a6765 74536571 seqStore::getSeq
│ │ │ │    0x000174b0 75656e63 65287061 7274292d 2d202069 uence(part)--  i
│ │ │ │    0x000174c0 69642025 75206d6f 72652074 68616e20 id %u more than 
│ │ │ │ @@ -610,15 +610,15 @@
│ │ │ │    0x000175f0 20736571 75656e63 6573202d 2d202535  sequences -- %5
│ │ │ │    0x00017600 2e306620 73657175 656e6365 732f7365 .0f sequences/se
│ │ │ │    0x00017610 636f6e64 0d000000 766f6964 20626974 cond....void bit
│ │ │ │    0x00017620 5061636b 65644669 6c653a3a 70757442 PackedFile::putB
│ │ │ │    0x00017630 69747328 75696e74 36342c20 75696e74 its(uint64, uint
│ │ │ │    0x00017640 33322900 00000000 2f627569 6c642f6b 32)...../build/k
│ │ │ │    0x00017650 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00017660 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00017660 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00017670 2f6c6962 7574696c 2f626974 5061636b /libutil/bitPack
│ │ │ │    0x00017680 65644669 6c652e48 00000000 00000000 edFile.H........
│ │ │ │    0x00017690 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ │    0x000176a0 6528292d 2d202046 61696c65 6420746f e()--  Failed to
│ │ │ │    0x000176b0 2072656f 70656e20 27257327 20746f20  reopen '%s' to 
│ │ │ │    0x000176c0 77726974 65206461 74613a20 25730a00 write data: %s..
│ │ │ │    0x000176d0 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 39663863 31303332 62393630 64353930 9f8c1032b960d590
│ │ │ │ -  0x00000010 61316435 66353239 61396533 37643834 a1d5f529a9e37d84
│ │ │ │ -  0x00000020 64613737 35632e64 65627567 00000000 da775c.debug....
│ │ │ │ -  0x00000030 0429593f                            .)Y?
│ │ │ │ +  0x00000000 35396635 34383566 31643836 37636431 59f5485f1d867cd1
│ │ │ │ +  0x00000010 64393431 66353863 65336434 37393038 d941f58ce3d47908
│ │ │ │ +  0x00000020 36653130 33352e64 65627567 00000000 6e1035.debug....
│ │ │ │ +  0x00000030 72368f0a                            r6..
│ │ ├── ./usr/bin/parseSNP
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 24b9fe9e8e24e9ca32b48d5eeeef2b7d330bd306
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 5481610f0b861da73ea434bc9125685f15da5b1e
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -148,15 +148,15 @@
│ │ │ │  abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_-
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -167,15 +167,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -247,15 +247,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -b9fe9e8e24e9ca32b48d5eeeef2b7d330bd306.debug
│ │ │ │ +81610f0b861da73ea434bc9125685f15da5b1e.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -259,15 +259,15 @@
│ │ │ │    0x0000d000 25730a00 3b696e74 726f6e3d 25730a00 %s..;intron=%s..
│ │ │ │    0x0000d010 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000d020 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000d030 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000d040 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000d050 76657273 65000000 2f627569 6c642f6b verse.../build/k
│ │ │ │    0x0000d060 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000d070 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000d070 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000d080 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000d090 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x0000d0a0 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x0000d0b0 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x0000d0c0 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x0000d0d0 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x0000d0e0 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -329,15 +329,15 @@
│ │ │ │    0x0000d460 41206c69 6e652061 74206279 74652025 A line at byte %
│ │ │ │    0x0000d470 6c750a00 00000000 766f6964 2073696d lu......void sim
│ │ │ │    0x0000d480 34706f6c 6973683a 3a733470 5f6c696e 4polish::s4p_lin
│ │ │ │    0x0000d490 6573546f 506f6c69 73685334 44422875 esToPolishS4DB(u
│ │ │ │    0x0000d4a0 696e7433 322c2075 696e7433 322c2063 int32, uint32, c
│ │ │ │    0x0000d4b0 6861722a 2a2c2075 696e7433 322a2900 har**, uint32*).
│ │ │ │    0x0000d4c0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000d4d0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000d4d0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000d4e0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000d4f0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000d500 706f6c69 73682d73 7472696e 67746f70 polish-stringtop
│ │ │ │    0x0000d510 6f6c6973 682e4300 73696d34 706f6c69 olish.C.sim4poli
│ │ │ │    0x0000d520 73683a3a 7334705f 6c696e65 73546f50 sh::s4p_linesToP
│ │ │ │    0x0000d530 6f6c6973 68533444 4228292d 2d20496e olishS4DB()-- In
│ │ │ │    0x0000d540 76616c69 64207369 6d346462 20666f72 valid sim4db for
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 62396665 39653865 32346539 63613332 b9fe9e8e24e9ca32
│ │ │ │ -  0x00000010 62343864 35656565 65663262 37643333 b48d5eeeef2b7d33
│ │ │ │ -  0x00000020 30626433 30362e64 65627567 00000000 0bd306.debug....
│ │ │ │ -  0x00000030 577146de                            WqF.
│ │ │ │ +  0x00000000 38313631 30663062 38363164 61373365 81610f0b861da73e
│ │ │ │ +  0x00000010 61343334 62633931 32353638 35663135 a434bc9125685f15
│ │ │ │ +  0x00000020 64613562 31652e64 65627567 00000000 da5b1e.debug....
│ │ │ │ +  0x00000030 d3c9410d                            ..A.
│ │ ├── ./usr/bin/pickBestPolish
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: f05b30b0bccec62dc125eda16b52a728aa6c1762
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 10df2f14499506c417ee3d88cc30276c2bb97174
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -93,15 +93,15 @@
│ │ │ │  ?char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -129,15 +129,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -210,15 +210,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -5b30b0bccec62dc125eda16b52a728aa6c1762.debug
│ │ │ │ +df2f14499506c417ee3d88cc30276c2bb97174.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -54,15 +54,15 @@
│ │ │ │    0x0000e330 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000e340 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000e350 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000e360 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000e370 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000e380 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000e390 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000e3a0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000e3a0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000e3b0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000e3c0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000e3d0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000e3e0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000e3f0 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000e400 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000e410 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -187,15 +187,15 @@
│ │ │ │    0x0000eb80 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000eb90 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000eba0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000ebb0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000ebc0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000ebd0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000ebe0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000ebf0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000ebf0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000ec00 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000ec10 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000ec20 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000ec30 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000ec40 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000ec50 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000ec60 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 35623330 62306263 63656336 32646331 5b30b0bccec62dc1
│ │ │ │ -  0x00000010 32356564 61313662 35326137 32386161 25eda16b52a728aa
│ │ │ │ -  0x00000020 36633137 36322e64 65627567 00000000 6c1762.debug....
│ │ │ │ -  0x00000030 6678b3e3                            fx..
│ │ │ │ +  0x00000000 64663266 31343439 39353036 63343137 df2f14499506c417
│ │ │ │ +  0x00000010 65653364 38386363 33303237 36633262 ee3d88cc30276c2b
│ │ │ │ +  0x00000020 62393731 37342e64 65627567 00000000 b97174.debug....
│ │ │ │ +  0x00000030 d137297e                            .7)~
│ │ ├── ./usr/bin/pickUniquePolish
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 4eb3ae8ecbcaac5d24c12658eaee7b99a571d8bc
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: d4b11b0ed7ad6d472ba206075b2d8221d217169f
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -98,15 +98,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -134,15 +134,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -215,15 +215,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -b3ae8ecbcaac5d24c12658eaee7b99a571d8bc.debug
│ │ │ │ +b11b0ed7ad6d472ba206075b2d8221d217169f.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -61,15 +61,15 @@
│ │ │ │    0x0000b3a0 00202d2d 00203c2d 00202d3e 00554e4b . --. <-. ->.UNK
│ │ │ │    0x0000b3b0 4e4f574e 00657272 6f720061 626f7274 NOWN.error.abort
│ │ │ │    0x0000b3c0 65640069 6e747261 63746162 6c650075 ed.intractable.u
│ │ │ │    0x0000b3d0 6e6b6e6f 776e0072 65766572 73650066 nknown.reverse.f
│ │ │ │    0x0000b3e0 6f727761 72640063 6f6d706c 656d656e orward.complemen
│ │ │ │    0x0000b3f0 74000000 00000000 2f627569 6c642f6b t......./build/k
│ │ │ │    0x0000b400 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000b410 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000b410 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000b420 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000b430 6973682f 73696d34 706f6c69 73682d70 ish/sim4polish-p
│ │ │ │    0x0000b440 6f6c6973 68746f73 7472696e 672e4300 olishtostring.C.
│ │ │ │    0x0000b450 73696d34 72656164 65723a20 556e6b6e sim4reader: Unkn
│ │ │ │    0x0000b460 6f776e20 6d617463 684f7269 656e7461 own matchOrienta
│ │ │ │    0x0000b470 74696f6e 20272575 2720696e 20707269 tion '%u' in pri
│ │ │ │    0x0000b480 6e74506f 6c697368 28290a00 00000000 ntPolish()......
│ │ │ │ @@ -195,15 +195,15 @@
│ │ │ │    0x0000bc00 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000bc10 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000bc20 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000bc30 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000bc40 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000bc50 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000bc60 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000bc70 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000bc70 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000bc80 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000bc90 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000bca0 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000bcb0 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000bcc0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000bcd0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000bce0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 62336165 38656362 63616163 35643234 b3ae8ecbcaac5d24
│ │ │ │ -  0x00000010 63313236 35386561 65653762 39396135 c12658eaee7b99a5
│ │ │ │ -  0x00000020 37316438 62632e64 65627567 00000000 71d8bc.debug....
│ │ │ │ -  0x00000030 ff983c26                            ..<&
│ │ │ │ +  0x00000000 62313162 30656437 61643664 34373262 b11b0ed7ad6d472b
│ │ │ │ +  0x00000010 61323036 30373562 32643832 32316432 a206075b2d8221d2
│ │ │ │ +  0x00000020 31373136 39662e64 65627567 00000000 17169f.debug....
│ │ │ │ +  0x00000030 889855b1                            ..U.
│ │ ├── ./usr/bin/plotCoverageVsIdentity
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 3a2d0a835e51f94d7c858ace3478e6e3b0442e0d
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 90836c18102fa75a01d71a1686d7834cc57b039f
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -99,15 +99,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -118,15 +118,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -199,15 +199,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -2d0a835e51f94d7c858ace3478e6e3b0442e0d.debug
│ │ │ │ +836c18102fa75a01d71a1686d7834cc57b039f.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -86,15 +86,15 @@
│ │ │ │    0x0000a530 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000a540 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000a550 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000a560 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000a570 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000a580 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000a590 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000a5a0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000a5a0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000a5b0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000a5c0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000a5d0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000a5e0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000a5f0 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000a600 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000a610 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -157,15 +157,15 @@
│ │ │ │    0x0000a9a0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000a9b0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000a9c0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000a9d0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000a9e0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000a9f0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000aa00 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000aa10 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000aa10 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000aa20 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000aa30 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000aa40 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000aa50 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000aa60 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000aa70 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000aa80 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 32643061 38333565 35316639 34643763 2d0a835e51f94d7c
│ │ │ │ -  0x00000010 38353861 63653334 37386536 65336230 858ace3478e6e3b0
│ │ │ │ -  0x00000020 34343265 30642e64 65627567 00000000 442e0d.debug....
│ │ │ │ -  0x00000030 e6637578                            .cux
│ │ │ │ +  0x00000000 38333663 31383130 32666137 35613031 836c18102fa75a01
│ │ │ │ +  0x00000010 64373161 31363836 64373833 34636335 d71a1686d7834cc5
│ │ │ │ +  0x00000020 37623033 39662e64 65627567 00000000 7b039f.debug....
│ │ │ │ +  0x00000030 e3583e72                            .X>r
│ │ ├── ./usr/bin/realignPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 8f973d256f6ffeefca8de60066d07ff25b5b4dc3
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 0c02f77faa5eb685a2b481a7243122badbce3029
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -194,15 +194,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -213,15 +213,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -253,15 +253,15 @@
│ │ │ │  Parent=sim4db
│ │ │ │  Parent=sim4db%u
│ │ │ │  Target=%s %u %u %c
│ │ │ │  nMatches=
│ │ │ │  nMatches=%u
│ │ │ │  intron=%s
│ │ │ │  seqCache::loadAllSequences()-- Failed to load iid %u.
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqFactory.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqFactory.C
│ │ │ │  seqFactory::registerFile()--  Wow!  You registered lots of files!  Now fix %s at line %d.
│ │ │ │  seqFactory::registerFile()--  Cannot determine type of file '%s'.  Tried:
│ │ │ │  seqFactory::registerFile()--         '%s'
│ │ │ │  fastaFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(part)-- ERROR2: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(full)-- ERROR1: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │ @@ -274,15 +274,15 @@
│ │ │ │  fastaFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │  fastaFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastaidx
│ │ │ │  7seqFile
│ │ │ │  9fastaFile
│ │ │ │  kmerFastaFileIdxfastaStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastaStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastaStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastaStdin.C
│ │ │ │  fastaStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastaStdin::loadNextSequence(part)-- ERROR: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaStdin::getSequenceLength()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastaStdin::getSequenceLength(uint32)
│ │ │ │  fastaStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ @@ -292,15 +292,15 @@
│ │ │ │  10fastaStdin
│ │ │ │  fastqFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(part)-- ERROR2: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(full)-- ERROR1: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence()-- ERROR: sequence is too long; must be less than 4 Gbp.
│ │ │ │  virtual bool fastqFile::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqFile.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqFile.C
│ │ │ │  (_rb->eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- open of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- magic mismatch.
│ │ │ │  fastqFile::constructIndex()-- stat mismatch.
│ │ │ │  fastqFile::constructIndex()-- ERROR3: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │ @@ -308,15 +308,15 @@
│ │ │ │  (ib.eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastqidx
│ │ │ │  REALLOC len=%u from %u to %u
│ │ │ │  9fastqFile
│ │ │ │  fastqStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastqStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqStdin.C
│ │ │ │  fastqStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastqStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastqStdin::loadNextSequence(part)-- ERROR: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  bool fastqStdin::loadNextSequence(char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │  fastqStdin::getSequence()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastqStdin::getSequenceLength(uint32)
│ │ │ │  fastqStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │ @@ -325,23 +325,23 @@
│ │ │ │  sLen == _block[block]._pos
│ │ │ │  sPos == _block[block]._pos
│ │ │ │  _isReadOnly == false
│ │ │ │  seqStore::seqStore()--  Failed to open '%s': %s
│ │ │ │  seqStore::seqStore()--  Failed to read index from '%s': %s
│ │ │ │  seqStore::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  virtual bool seqStore::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqStore.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqStore.C
│ │ │ │  _bpf->tell() == _block[block]._bpf * 2
│ │ │ │  seqStore::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  seqStore::getSequence(part)--  for iid %u; invalid bgn=%u end=%u; seqLen=%u
│ │ │ │  virtual bool seqStore::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  constructSeqStore()-- constructing seqStore '%s' from seqCache '%s' of type '%s'.
│ │ │ │   reading sequences %7.0f sequences -- %5.0f sequences/second
│ │ │ │  void bitPackedFile::putBits(uint64, uint32)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libutil/bitPackedFile.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libutil/bitPackedFile.H
│ │ │ │  constructSeqStore()--  Failed to reopen '%s' to write data: %s
│ │ │ │  constructSeqStore()--  Failed to write data to '%s': %s
│ │ │ │  constructSeqStore()-- seqStore '%s' constructed (%u sequences, %lu ACGT letters, %u ACGT blocks, %u GAP blocks).
│ │ │ │  8seqStore
│ │ │ │  kmerSeqStoreFilehalign::rsnake()-- TROUBLE!!! startx:  %5d,  starty:  %5d
│ │ │ │  halign::rsnake()-- TROUBLE!!! x:  %5d,  y:  %5d
│ │ │ │  halign::align_path()-- warning: something wrong when aligning.
│ │ │ │ @@ -424,15 +424,15 @@
│ │ │ │  [        --]
│ │ │ │  [         -]
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -973d256f6ffeefca8de60066d07ff25b5b4dc3.debug
│ │ │ │ +02f77faa5eb685a2b481a7243122badbce3029.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -122,15 +122,15 @@
│ │ │ │    0x00017770 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x00017780 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x00017790 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x000177a0 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x000177b0 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x000177c0 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x000177d0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000177e0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000177e0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000177f0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x00017800 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x00017810 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x00017820 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x00017830 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x00017840 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x00017850 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -193,15 +193,15 @@
│ │ │ │    0x00017be0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x00017bf0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x00017c00 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x00017c10 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x00017c20 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x00017c30 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x00017c40 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00017c50 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00017c50 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00017c60 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x00017c70 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x00017c80 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x00017c90 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x00017ca0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x00017cb0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x00017cc0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ │ @@ -315,15 +315,15 @@
│ │ │ │    0x00018380 63f8feff 63f8feff 63f8feff 63f8feff c...c...c...c...
│ │ │ │    0x00018390 63f8feff 65fcfeff 63f8feff 71fcfeff c...e...c...q...
│ │ │ │    0x000183a0 63f8feff 7dfcfeff 73657143 61636865 c...}...seqCache
│ │ │ │    0x000183b0 3a3a6c6f 6164416c 6c536571 75656e63 ::loadAllSequenc
│ │ │ │    0x000183c0 65732829 2d2d2046 61696c65 6420746f es()-- Failed to
│ │ │ │    0x000183d0 206c6f61 64206969 64202575 2e0a0000  load iid %u....
│ │ │ │    0x000183e0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000183f0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000183f0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00018400 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00018410 73657146 6163746f 72792e43 00000000 seqFactory.C....
│ │ │ │    0x00018420 73657146 6163746f 72793a3a 72656769 seqFactory::regi
│ │ │ │    0x00018430 73746572 46696c65 28292d2d 2020576f sterFile()--  Wo
│ │ │ │    0x00018440 77212020 596f7520 72656769 73746572 w!  You register
│ │ │ │    0x00018450 6564206c 6f747320 6f662066 696c6573 ed lots of files
│ │ │ │    0x00018460 2120204e 6f772066 69782025 73206174 !  Now fix %s at
│ │ │ │ @@ -404,15 +404,15 @@
│ │ │ │    0x00018910 28292d2d 20455252 4f522120 20557365 ()-- ERROR!  Use
│ │ │ │    0x00018920 6420666f 72207261 6e646f6d 20616363 d for random acc
│ │ │ │    0x00018930 6573732e 0a000000 76697274 75616c20 ess.....virtual 
│ │ │ │    0x00018940 75696e74 33322066 61737461 53746469 uint32 fastaStdi
│ │ │ │    0x00018950 6e3a3a66 696e6428 636f6e73 74206368 n::find(const ch
│ │ │ │    0x00018960 61722a29 00000000 2f627569 6c642f6b ar*)..../build/k
│ │ │ │    0x00018970 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00018980 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00018980 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00018990 2f6c6962 7365712f 66617374 61537464 /libseq/fastaStd
│ │ │ │    0x000189a0 696e2e43 00000000 66617374 61537464 in.C....fastaStd
│ │ │ │    0x000189b0 696e3a3a 67657453 65717565 6e636528 in::getSequence(
│ │ │ │    0x000189c0 70617274 292d2d20 4552524f 52212020 part)-- ERROR!  
│ │ │ │    0x000189d0 55736564 20666f72 2072616e 646f6d20 Used for random 
│ │ │ │    0x000189e0 61636365 73732e0a 00000000 00000000 access..........
│ │ │ │    0x000189f0 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │ @@ -483,15 +483,15 @@
│ │ │ │    0x00018e00 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │    0x00018e10 74714669 6c653a3a 67657453 65717565 tqFile::getSeque
│ │ │ │    0x00018e20 6e636528 75696e74 33322c20 63686172 nce(uint32, char
│ │ │ │    0x00018e30 2a262c20 75696e74 3332262c 2075696e *&, uint32&, uin
│ │ │ │    0x00018e40 74333226 2c206368 61722a26 2c207569 t32&, char*&, ui
│ │ │ │    0x00018e50 6e743332 262c2075 696e7433 32262900 nt32&, uint32&).
│ │ │ │    0x00018e60 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00018e70 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00018e70 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00018e80 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00018e90 66617374 7146696c 652e4300 00000000 fastqFile.C.....
│ │ │ │    0x00018ea0 285f7262 2d3e656f 66282920 3d3d2074 (_rb->eof() == t
│ │ │ │    0x00018eb0 72756529 207c7c20 2878203d 3d20272b rue) || (x == '+
│ │ │ │    0x00018ec0 27290000 00000000 66617374 7146696c ')......fastqFil
│ │ │ │    0x00018ed0 653a3a63 6f6e7374 72756374 496e6465 e::constructInde
│ │ │ │    0x00018ee0 7828292d 2d207374 6174206f 66206669 x()-- stat of fi
│ │ │ │ @@ -536,15 +536,15 @@
│ │ │ │    0x00019150 696e3a3a 66696e64 28292d2d 20455252 in::find()-- ERR
│ │ │ │    0x00019160 4f522120 20557365 6420666f 72207261 OR!  Used for ra
│ │ │ │    0x00019170 6e646f6d 20616363 6573732e 0a000000 ndom access.....
│ │ │ │    0x00019180 76697274 75616c20 75696e74 33322066 virtual uint32 f
│ │ │ │    0x00019190 61737471 53746469 6e3a3a66 696e6428 astqStdin::find(
│ │ │ │    0x000191a0 636f6e73 74206368 61722a29 00000000 const char*)....
│ │ │ │    0x000191b0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000191c0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000191c0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000191d0 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x000191e0 66617374 71537464 696e2e43 00000000 fastqStdin.C....
│ │ │ │    0x000191f0 66617374 71537464 696e3a3a 67657453 fastqStdin::getS
│ │ │ │    0x00019200 65717565 6e636528 70617274 292d2d20 equence(part)-- 
│ │ │ │    0x00019210 4552524f 52212020 55736564 20666f72 ERROR!  Used for
│ │ │ │    0x00019220 2072616e 646f6d20 61636365 73732e0a  random access..
│ │ │ │    0x00019230 00000000 00000000 76697274 75616c20 ........virtual 
│ │ │ │ @@ -608,15 +608,15 @@
│ │ │ │    0x000195d0 626f6f6c 20736571 53746f72 653a3a67 bool seqStore::g
│ │ │ │    0x000195e0 65745365 7175656e 63652875 696e7433 etSequence(uint3
│ │ │ │    0x000195f0 322c2063 6861722a 262c2075 696e7433 2, char*&, uint3
│ │ │ │    0x00019600 32262c20 75696e74 3332262c 20636861 2&, uint32&, cha
│ │ │ │    0x00019610 722a262c 2075696e 74333226 2c207569 r*&, uint32&, ui
│ │ │ │    0x00019620 6e743332 26290000 2f627569 6c642f6b nt32&)../build/k
│ │ │ │    0x00019630 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00019640 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00019640 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00019650 2f6c6962 7365712f 73657153 746f7265 /libseq/seqStore
│ │ │ │    0x00019660 2e430000 00000000 5f627066 2d3e7465 .C......_bpf->te
│ │ │ │    0x00019670 6c6c2829 203d3d20 5f626c6f 636b5b62 ll() == _block[b
│ │ │ │    0x00019680 6c6f636b 5d2e5f62 7066202a 20320000 lock]._bpf * 2..
│ │ │ │    0x00019690 73657153 746f7265 3a3a6765 74536571 seqStore::getSeq
│ │ │ │    0x000196a0 75656e63 65287061 7274292d 2d202069 uence(part)--  i
│ │ │ │    0x000196b0 69642025 75206d6f 72652074 68616e20 id %u more than 
│ │ │ │ @@ -641,15 +641,15 @@
│ │ │ │    0x000197e0 20736571 75656e63 6573202d 2d202535  sequences -- %5
│ │ │ │    0x000197f0 2e306620 73657175 656e6365 732f7365 .0f sequences/se
│ │ │ │    0x00019800 636f6e64 0d000000 766f6964 20626974 cond....void bit
│ │ │ │    0x00019810 5061636b 65644669 6c653a3a 70757442 PackedFile::putB
│ │ │ │    0x00019820 69747328 75696e74 36342c20 75696e74 its(uint64, uint
│ │ │ │    0x00019830 33322900 00000000 2f627569 6c642f6b 32)...../build/k
│ │ │ │    0x00019840 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00019850 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00019850 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00019860 2f6c6962 7574696c 2f626974 5061636b /libutil/bitPack
│ │ │ │    0x00019870 65644669 6c652e48 00000000 00000000 edFile.H........
│ │ │ │    0x00019880 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ │    0x00019890 6528292d 2d202046 61696c65 6420746f e()--  Failed to
│ │ │ │    0x000198a0 2072656f 70656e20 27257327 20746f20  reopen '%s' to 
│ │ │ │    0x000198b0 77726974 65206461 74613a20 25730a00 write data: %s..
│ │ │ │    0x000198c0 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 39373364 32353666 36666665 65666361 973d256f6ffeefca
│ │ │ │ -  0x00000010 38646536 30303636 64303766 66323562 8de60066d07ff25b
│ │ │ │ -  0x00000020 35623464 63332e64 65627567 00000000 5b4dc3.debug....
│ │ │ │ -  0x00000030 644dc149                            dM.I
│ │ │ │ +  0x00000000 30326637 37666161 35656236 38356132 02f77faa5eb685a2
│ │ │ │ +  0x00000010 62343831 61373234 33313232 62616462 b481a7243122badb
│ │ │ │ +  0x00000020 63653330 32392e64 65627567 00000000 ce3029.debug....
│ │ │ │ +  0x00000030 c29bce49                            ...I
│ │ ├── ./usr/bin/removeDuplicate
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: b0113a64b0fa28ced0bfa4513bc863d6f95c27f1
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 6fcdec88fd2e4e58181fb886b6cc50de1a148bc0
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -84,15 +84,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -120,15 +120,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -201,15 +201,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -113a64b0fa28ced0bfa4513bc863d6f95c27f1.debug
│ │ │ │ +cdec88fd2e4e58181fb886b6cc50de1a148bc0.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -26,15 +26,15 @@
│ │ │ │    0x0000a170 6f6e3d25 730a0020 3f3f0020 3d3d0020 on=%s.. ??. ==. 
│ │ │ │    0x0000a180 2d2d0020 3c2d0020 2d3e0055 4e4b4e4f --. <-. ->.UNKNO
│ │ │ │    0x0000a190 574e0065 72726f72 0061626f 72746564 WN.error.aborted
│ │ │ │    0x0000a1a0 00696e74 72616374 61626c65 00756e6b .intractable.unk
│ │ │ │    0x0000a1b0 6e6f776e 00726576 65727365 00666f72 nown.reverse.for
│ │ │ │    0x0000a1c0 77617264 00636f6d 706c656d 656e7400 ward.complement.
│ │ │ │    0x0000a1d0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000a1e0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000a1e0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000a1f0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000a200 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000a210 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000a220 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000a230 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000a240 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000a250 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -159,15 +159,15 @@
│ │ │ │    0x0000a9c0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000a9d0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000a9e0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000a9f0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000aa00 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000aa10 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000aa20 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000aa30 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000aa30 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000aa40 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000aa50 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000aa60 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000aa70 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000aa80 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000aa90 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000aaa0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 31313361 36346230 66613238 63656430 113a64b0fa28ced0
│ │ │ │ -  0x00000010 62666134 35313362 63383633 64366639 bfa4513bc863d6f9
│ │ │ │ -  0x00000020 35633237 66312e64 65627567 00000000 5c27f1.debug....
│ │ │ │ -  0x00000030 96d515ec                            ....
│ │ │ │ +  0x00000000 63646563 38386664 32653465 35383138 cdec88fd2e4e5818
│ │ │ │ +  0x00000010 31666238 38366236 63633530 64653161 1fb886b6cc50de1a
│ │ │ │ +  0x00000020 31343862 63302e64 65627567 00000000 148bc0.debug....
│ │ │ │ +  0x00000030 59ce7e77                            Y.~w
│ │ ├── ./usr/bin/reportAlignmentDifferences
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: f151586738c883474adec2b8cdcc39e2a1c46785
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 7a6d73452f0ae5e2641e6fb5c60487cc2f6afb3e
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -136,15 +136,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -155,15 +155,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -236,15 +236,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -51586738c883474adec2b8cdcc39e2a1c46785.debug
│ │ │ │ +6d73452f0ae5e2641e6fb5c60487cc2f6afb3e.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -164,15 +164,15 @@
│ │ │ │    0x0000aa10 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000aa20 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000aa30 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000aa40 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000aa50 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000aa60 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000aa70 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000aa80 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000aa80 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000aa90 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000aaa0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000aab0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000aac0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000aad0 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000aae0 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000aaf0 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -235,15 +235,15 @@
│ │ │ │    0x0000ae80 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000ae90 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000aea0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000aeb0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000aec0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000aed0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000aee0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000aef0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000aef0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000af00 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000af10 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000af20 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000af30 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000af40 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000af50 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000af60 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 35313538 36373338 63383833 34373461 51586738c883474a
│ │ │ │ -  0x00000010 64656332 62386364 63633339 65326131 dec2b8cdcc39e2a1
│ │ │ │ -  0x00000020 63343637 38352e64 65627567 00000000 c46785.debug....
│ │ │ │ -  0x00000030 cd2c3838                            .,88
│ │ │ │ +  0x00000000 36643733 34353266 30616535 65323634 6d73452f0ae5e264
│ │ │ │ +  0x00000010 31653666 62356336 30343837 63633266 1e6fb5c60487cc2f
│ │ │ │ +  0x00000020 36616662 33652e64 65627567 00000000 6afb3e.debug....
│ │ │ │ +  0x00000030 92f58ebf                            ....
│ │ ├── ./usr/bin/sim4db
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: db9a49151883d4b146d55887d22813d550604b60
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: a026ca847e08868af9b7d5d3a8dba29de8cf8fc9
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -303,15 +303,15 @@
│ │ │ │  []A\A]A^A_
│ │ │ │  []A\A]A^A_
│ │ │ │  Couldn't write the output file '%s': %s
│ │ │ │  Couldn't open the output file '%s': %s
│ │ │ │  WARNING:  -cut adjusted to 0.0 (you gave %f)!
│ │ │ │  WARNING:  -cut adjusted to 1.0 (you gave %f)!
│ │ │ │  void sim4parameters::setSpacedSeed(char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/sim4parameters.H
│ │ │ │  strlen(z) < SPACED_SEED_MAX_LEN
│ │ │ │  usage: %s -genomic g.fasta -cdna c.fasta -output o.sim4db [options]
│ │ │ │         -v            print status to stderr while running
│ │ │ │         -V            print script lines (stderr) as they are processed
│ │ │ │         -YN           print script lines (to given file) as they are processed, annotated with yes/no
│ │ │ │         -cdna         use these cDNA sequences
│ │ │ │         -genomic      use these genomic sequences
│ │ │ │ @@ -376,54 +376,54 @@
│ │ │ │  Two sequences are not really similar.
│ │ │ │  Sim4::align_path()-- warning: something wrong when aligning.
│ │ │ │  Please try exact phase 1.
│ │ │ │  Something wrong when dividing
│ │ │ │  sim4::link()-- ERROR; mspManager parameters not set!  This is an algorithm error.
│ │ │ │    GEN f=%8d t=%8d  EST f=%8d t=%8d   flag=%d
│ │ │ │  void Sim4::trim_polyA_align(Sim4::edit_script_list**, Exon*, Exon**, int, int*, char*, char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/poly.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/poly.C
│ │ │ │  trim_polyA_align(): Corrupted exon list, cannot find the previous exon (remove entire script).
│ │ │ │  trim_polyA_align(): Corrupted exon list, cannot find the previous exon (frEST).
│ │ │ │  void Sim4::trim_polyT_align(Sim4::edit_script_list**, Exon**, int, int*, char*, char*)
│ │ │ │  sig->pos2 > 1
│ │ │ │  _estLen-sig->pos2 >= 0
│ │ │ │  void Sim4::adjustBoundariesOfMarginalExons(Exon*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/sim4b1a.C
│ │ │ │    GEN f=%8d t=%8d  EST f=%8d t=%8d   flag=%d <- tried to find previous of this one
│ │ │ │  SIM4_block1(): Corrupted exon list, cannot find the previous exon.
│ │ │ │  Xextend_bw -- Xextend_bw NOT OPTIMIZED
│ │ │ │  Xextend_bw -- Xextend_fw NOT OPTIMIZED
│ │ │ │  The seed can only contain 0, 1, or x, or any other characters
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/sim4b1_s.C
│ │ │ │  mss_t::mss_t(char*)
│ │ │ │  masknum <= 64
│ │ │ │  Xt[j]+CCf[j]!=0
│ │ │ │  CCb[j]+Xt[j]!=0
│ │ │ │  ERROR:  Positive and negative donor model lengths differ
│ │ │ │  ERROR:  Positive and negative acceptor model lengths differ
│ │ │ │  void Sim4::splice_donor(char*, char*, int, int, double*, double*, double**, double**, int**, int**)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/splice.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/splice.C
│ │ │ │  void Sim4::splice_donor_uni(char*, char*, int, int, double*, double**, int**)
│ │ │ │  void Sim4::splice_acceptor(char*, char*, int, int, double*, double*, double**, double**, int**, int**)
│ │ │ │  void Sim4::splice_acceptor_uni(char*, char*, int, int, double*, double**, int**)
│ │ │ │  Unrecognized splice model (%d). Using original.
│ │ │ │  ?unknown type in bld_table: %d
│ │ │ │  sim4b1.c: Inconsistency. Check exon orientation at complementation.
│ │ │ │  void Sim4::merge(Exon**, Exon**)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/util.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/util.C
│ │ │ │  sim4b1.c: intron orientation not initialized.
│ │ │ │  tmp1!=NULL
│ │ │ │  ?char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -464,15 +464,15 @@
│ │ │ │  ERROR:  Bad character %c in subscript conversion
│ │ │ │  WARNING:  prob = %.4f  pos = %d in  Full_Window_Prob
│ │ │ │  ERROR:  calloc failed  %lu x %lu
│ │ │ │  ERROR:  malloc failed  %lu  bytes
│ │ │ │  ERROR:  realloc failed  %lu  bytes
│ │ │ │  Bad ICM version = %d  should be %d
│ │ │ │  Bad ID_STRING_LEN = %d  should be %d
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4core/glimmerSplice.C
│ │ │ │  ERROR reading icm node = %d  period = %d
│ │ │ │  ERROR reading mut_info_pos for node = %d  period = %d
│ │ │ │  ERROR:  Too few nodes for periodicity = %d
│ │ │ │  Error: Could not open Glimmer model file for reading (%s).
│ │ │ │  ERROR:  String "%s" too short in Score_Window
│ │ │ │  num_node = %d
│ │ │ │    in file  %s
│ │ │ │ @@ -491,15 +491,15 @@
│ │ │ │  s4p_compareExons()-- Can't allocate %u + %u words for counting exons.
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -531,15 +531,15 @@
│ │ │ │  Parent=sim4db
│ │ │ │  Parent=sim4db%u
│ │ │ │  Target=%s %u %u %c
│ │ │ │  nMatches=
│ │ │ │  nMatches=%u
│ │ │ │  intron=%s
│ │ │ │  seqCache::loadAllSequences()-- Failed to load iid %u.
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqFactory.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqFactory.C
│ │ │ │  seqFactory::registerFile()--  Wow!  You registered lots of files!  Now fix %s at line %d.
│ │ │ │  seqFactory::registerFile()--  Cannot determine type of file '%s'.  Tried:
│ │ │ │  seqFactory::registerFile()--         '%s'
│ │ │ │  fastaFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(part)-- ERROR2: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastaFile::getSequence(full)-- ERROR1: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │ @@ -552,15 +552,15 @@
│ │ │ │  fastaFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │  fastaFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastaidx
│ │ │ │  7seqFile
│ │ │ │  9fastaFile
│ │ │ │  kmerFastaFileIdxfastaStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastaStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastaStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastaStdin.C
│ │ │ │  fastaStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastaStdin::loadNextSequence(part)-- ERROR: In %s, expected '>' at beginning of defline, got '%c' instead.
│ │ │ │  fastaStdin::getSequenceLength()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastaStdin::getSequenceLength(uint32)
│ │ │ │  fastaStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ @@ -570,15 +570,15 @@
│ │ │ │  10fastaStdin
│ │ │ │  fastqFile::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(part)-- ERROR2: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  fastqFile::getSequence(full)-- ERROR1: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::getSequence()-- ERROR: sequence is too long; must be less than 4 Gbp.
│ │ │ │  virtual bool fastqFile::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqFile.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqFile.C
│ │ │ │  (_rb->eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- open of file '%s' failed: %s
│ │ │ │  fastqFile::constructIndex()-- magic mismatch.
│ │ │ │  fastqFile::constructIndex()-- stat mismatch.
│ │ │ │  fastqFile::constructIndex()-- ERROR3: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  fastqFile::constructIndex()-- ERROR: In %s, sequence '%s' is too long.  Maximum length is %u bases.
│ │ │ │ @@ -586,15 +586,15 @@
│ │ │ │  (ib.eof() == true) || (x == '+')
│ │ │ │  fastqFile::constructIndex()-- stat() of file '%s' failed: %s
│ │ │ │  .fastqidx
│ │ │ │  REALLOC len=%u from %u to %u
│ │ │ │  9fastqFile
│ │ │ │  fastqStdin::find()-- ERROR!  Used for random access.
│ │ │ │  virtual uint32 fastqStdin::find(const char*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/fastqStdin.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/fastqStdin.C
│ │ │ │  fastqStdin::getSequence(part)-- ERROR!  Used for random access.
│ │ │ │  virtual bool fastqStdin::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  fastqStdin::loadNextSequence(part)-- ERROR: In %s, expected '@' at beginning of defline, got '%c' instead.
│ │ │ │  bool fastqStdin::loadNextSequence(char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │  fastqStdin::getSequence()-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │  virtual uint32 fastqStdin::getSequenceLength(uint32)
│ │ │ │  fastqStdin::getSequence(full)-- ERROR!  Used for random access.  Requested iid=%u, at iid=%u
│ │ │ │ @@ -603,23 +603,23 @@
│ │ │ │  sLen == _block[block]._pos
│ │ │ │  sPos == _block[block]._pos
│ │ │ │  _isReadOnly == false
│ │ │ │  seqStore::seqStore()--  Failed to open '%s': %s
│ │ │ │  seqStore::seqStore()--  Failed to read index from '%s': %s
│ │ │ │  seqStore::getSequence(full)--  iid %u more than number of sequences %u
│ │ │ │  virtual bool seqStore::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libseq/seqStore.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libseq/seqStore.C
│ │ │ │  _bpf->tell() == _block[block]._bpf * 2
│ │ │ │  seqStore::getSequence(part)--  iid %u more than number of sequences %u
│ │ │ │  seqStore::getSequence(part)--  for iid %u; invalid bgn=%u end=%u; seqLen=%u
│ │ │ │  virtual bool seqStore::getSequence(uint32, uint32, uint32, char*)
│ │ │ │  constructSeqStore()-- constructing seqStore '%s' from seqCache '%s' of type '%s'.
│ │ │ │   reading sequences %7.0f sequences -- %5.0f sequences/second
│ │ │ │  void bitPackedFile::putBits(uint64, uint32)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libutil/bitPackedFile.H
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libutil/bitPackedFile.H
│ │ │ │  constructSeqStore()--  Failed to reopen '%s' to write data: %s
│ │ │ │  constructSeqStore()--  Failed to write data to '%s': %s
│ │ │ │  constructSeqStore()-- seqStore '%s' constructed (%u sequences, %lu ACGT letters, %u ACGT blocks, %u GAP blocks).
│ │ │ │  8seqStore
│ │ │ │  kmerSeqStoreFile/XXXXXX
│ │ │ │  Couldn't open() '%s'
│ │ │ │  Couldn't fstat() '%s'
│ │ │ │ @@ -723,15 +723,15 @@
│ │ │ │  ( 0 1 23 10000 l( 1 3 21 6544 l( 3 3 20 3573 l( 5 3 16 2146 l( 7 -1 -1 1295 l r ) r( 8 -1 -1 851 l r ) ) r( 6 -1 -1 1427 l r ) ) r( 4 1 21 2971 l( 15 1 20 1914 l( 17 -1 -1 1009 l r ) r( 18 -1 -1 905 l r ) ) r( 16 -1 -1 1057 l r ) ) ) r( 2 -1 -1 3456 l r ) )
│ │ │ │  ( 0 2 4 10000 l( 1 2 9 7841 l( 3 0 8 5666 l( 5 0 3 3977 l( 7 0 7 2186 l( 9 -1 -1 995 l r ) r( 10 -1 -1 1191 l r ) ) r( 8 3 10 1791 l( 15 -1 -1 931 l r ) r( 16 -1 -1 860 l r ) ) ) r( 6 -1 -1 1689 l r ) ) r( 4 -1 -1 2175 l r ) ) r( 2 -1 -1 2159 l r ) )
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -9a49151883d4b146d55887d22813d550604b60.debug
│ │ │ │ +26ca847e08868af9b7d5d3a8dba29de8cf8fc9.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -12,15 +12,15 @@
│ │ │ │    0x00046090 5741524e 494e473a 20202d63 75742061 WARNING:  -cut a
│ │ │ │    0x000460a0 646a7573 74656420 746f2031 2e302028 djusted to 1.0 (
│ │ │ │    0x000460b0 796f7520 67617665 20256629 210a0000 you gave %f)!...
│ │ │ │    0x000460c0 766f6964 2073696d 34706172 616d6574 void sim4paramet
│ │ │ │    0x000460d0 6572733a 3a736574 53706163 65645365 ers::setSpacedSe
│ │ │ │    0x000460e0 65642863 6861722a 29000000 00000000 ed(char*).......
│ │ │ │    0x000460f0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00046100 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00046100 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00046110 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x00046120 2f73696d 34636f72 652f7369 6d347061 /sim4core/sim4pa
│ │ │ │    0x00046130 72616d65 74657273 2e480000 00000000 rameters.H......
│ │ │ │    0x00046140 7374726c 656e287a 29203c20 53504143 strlen(z) < SPAC
│ │ │ │    0x00046150 45445f53 4545445f 4d41585f 4c454e00 ED_SEED_MAX_LEN.
│ │ │ │    0x00046160 75736167 653a2025 73202d67 656e6f6d usage: %s -genom
│ │ │ │    0x00046170 69632067 2e666173 7461202d 63646e61 ic g.fasta -cdna
│ │ │ │ @@ -297,15 +297,15 @@
│ │ │ │    0x00047260 766f6964 2053696d 343a3a74 72696d5f void Sim4::trim_
│ │ │ │    0x00047270 706f6c79 415f616c 69676e28 53696d34 polyA_align(Sim4
│ │ │ │    0x00047280 3a3a6564 69745f73 63726970 745f6c69 ::edit_script_li
│ │ │ │    0x00047290 73742a2a 2c204578 6f6e2a2c 2045786f st**, Exon*, Exo
│ │ │ │    0x000472a0 6e2a2a2c 20696e74 2c20696e 742a2c20 n**, int, int*, 
│ │ │ │    0x000472b0 63686172 2a2c2063 6861722a 29000000 char*, char*)...
│ │ │ │    0x000472c0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000472d0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000472d0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000472e0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x000472f0 2f73696d 34636f72 652f706f 6c792e43 /sim4core/poly.C
│ │ │ │    0x00047300 00000000 00000000 7472696d 5f706f6c ........trim_pol
│ │ │ │    0x00047310 79415f61 6c69676e 28293a20 436f7272 yA_align(): Corr
│ │ │ │    0x00047320 75707465 64206578 6f6e206c 6973742c upted exon list,
│ │ │ │    0x00047330 2063616e 6e6f7420 66696e64 20746865  cannot find the
│ │ │ │    0x00047340 20707265 76696f75 73206578 6f6e2028  previous exon (
│ │ │ │ @@ -328,15 +328,15 @@
│ │ │ │    0x00047450 3e706f73 32203e20 31005f65 73744c65 >pos2 > 1._estLe
│ │ │ │    0x00047460 6e2d7369 672d3e70 6f733220 3e3d2030 n-sig->pos2 >= 0
│ │ │ │    0x00047470 00000000 00000000 766f6964 2053696d ........void Sim
│ │ │ │    0x00047480 343a3a61 646a7573 74426f75 6e646172 4::adjustBoundar
│ │ │ │    0x00047490 6965734f 664d6172 67696e61 6c45786f iesOfMarginalExo
│ │ │ │    0x000474a0 6e732845 786f6e2a 29000000 00000000 ns(Exon*).......
│ │ │ │    0x000474b0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000474c0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000474c0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000474d0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x000474e0 2f73696d 34636f72 652f7369 6d346231 /sim4core/sim4b1
│ │ │ │    0x000474f0 612e4300 00000000 20204745 4e20663d a.C.....  GEN f=
│ │ │ │    0x00047500 25386420 743d2538 64202045 53542066 %8d t=%8d  EST f
│ │ │ │    0x00047510 3d253864 20743d25 38642020 20666c61 =%8d t=%8d   fla
│ │ │ │    0x00047520 673d2564 203c2d20 74726965 6420746f g=%d <- tried to
│ │ │ │    0x00047530 2066696e 64207072 6576696f 7573206f  find previous o
│ │ │ │ @@ -352,15 +352,15 @@
│ │ │ │    0x000475d0 7874656e 645f6677 204e4f54 204f5054 xtend_fw NOT OPT
│ │ │ │    0x000475e0 494d495a 45440a00 54686520 73656564 IMIZED..The seed
│ │ │ │    0x000475f0 2063616e 206f6e6c 7920636f 6e746169  can only contai
│ │ │ │    0x00047600 6e20302c 20312c20 6f722078 2c206f72 n 0, 1, or x, or
│ │ │ │    0x00047610 20616e79 206f7468 65722063 68617261  any other chara
│ │ │ │    0x00047620 63746572 73000000 2f627569 6c642f6b cters.../build/k
│ │ │ │    0x00047630 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x00047640 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x00047640 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x00047650 2f6c6962 73696d34 2f73696d 34636f72 /libsim4/sim4cor
│ │ │ │    0x00047660 652f7369 6d346231 5f732e43 006d7373 e/sim4b1_s.C.mss
│ │ │ │    0x00047670 5f743a3a 6d73735f 74286368 61722a29 _t::mss_t(char*)
│ │ │ │    0x00047680 006d6173 6b6e756d 203c3d20 36340025 .masknum <= 64.%
│ │ │ │    0x00047690 732f2573 0058745b 6a5d2b43 43665b6a s/%s.Xt[j]+CCf[j
│ │ │ │    0x000476a0 5d213d30 00434362 5b6a5d2b 58745b6a ]!=0.CCb[j]+Xt[j
│ │ │ │    0x000476b0 5d213d30 00000000 4552524f 523a2020 ]!=0....ERROR:  
│ │ │ │ @@ -375,15 +375,15 @@
│ │ │ │    0x00047740 343a3a73 706c6963 655f646f 6e6f7228 4::splice_donor(
│ │ │ │    0x00047750 63686172 2a2c2063 6861722a 2c20696e char*, char*, in
│ │ │ │    0x00047760 742c2069 6e742c20 646f7562 6c652a2c t, int, double*,
│ │ │ │    0x00047770 20646f75 626c652a 2c20646f 75626c65  double*, double
│ │ │ │    0x00047780 2a2a2c20 646f7562 6c652a2a 2c20696e **, double**, in
│ │ │ │    0x00047790 742a2a2c 20696e74 2a2a2900 00000000 t**, int**).....
│ │ │ │    0x000477a0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000477b0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000477b0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000477c0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x000477d0 2f73696d 34636f72 652f7370 6c696365 /sim4core/splice
│ │ │ │    0x000477e0 2e430000 00000000 766f6964 2053696d .C......void Sim
│ │ │ │    0x000477f0 343a3a73 706c6963 655f646f 6e6f725f 4::splice_donor_
│ │ │ │    0x00047800 756e6928 63686172 2a2c2063 6861722a uni(char*, char*
│ │ │ │    0x00047810 2c20696e 742c2069 6e742c20 646f7562 , int, int, doub
│ │ │ │    0x00047820 6c652a2c 20646f75 626c652a 2a2c2069 le*, double**, i
│ │ │ │ @@ -567,15 +567,15 @@
│ │ │ │    0x00048340 69737465 6e63792e 20436865 636b2065 istency. Check e
│ │ │ │    0x00048350 786f6e20 6f726965 6e746174 696f6e20 xon orientation 
│ │ │ │    0x00048360 61742063 6f6d706c 656d656e 74617469 at complementati
│ │ │ │    0x00048370 6f6e2e00 00000000 766f6964 2053696d on......void Sim
│ │ │ │    0x00048380 343a3a6d 65726765 2845786f 6e2a2a2c 4::merge(Exon**,
│ │ │ │    0x00048390 2045786f 6e2a2a29 00000000 00000000  Exon**)........
│ │ │ │    0x000483a0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x000483b0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x000483b0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x000483c0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x000483d0 2f73696d 34636f72 652f7574 696c2e43 /sim4core/util.C
│ │ │ │    0x000483e0 00000000 00000000 73696d34 62312e63 ........sim4b1.c
│ │ │ │    0x000483f0 3a20696e 74726f6e 206f7269 656e7461 : intron orienta
│ │ │ │    0x00048400 74696f6e 206e6f74 20696e69 7469616c tion not initial
│ │ │ │    0x00048410 697a6564 2e00746d 7031213d 4e554c4c ized..tmp1!=NULL
│ │ │ │    0x00048420 00000000 00000000 01000000 00000000 ................
│ │ │ │ @@ -592,15 +592,15 @@
│ │ │ │    0x000484d0 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x000484e0 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x000484f0 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x00048500 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x00048510 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x00048520 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x00048530 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00048540 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00048540 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00048550 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x00048560 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x00048570 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x00048580 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x00048590 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x000485a0 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x000485b0 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -802,15 +802,15 @@
│ │ │ │    0x000491f0 256c7520 20627974 65730000 00000000 %lu  bytes......
│ │ │ │    0x00049200 42616420 49434d20 76657273 696f6e20 Bad ICM version 
│ │ │ │    0x00049210 3d202564 20207368 6f756c64 20626520 = %d  should be 
│ │ │ │    0x00049220 25640a00 00000000 42616420 49445f53 %d......Bad ID_S
│ │ │ │    0x00049230 5452494e 475f4c45 4e203d20 25642020 TRING_LEN = %d  
│ │ │ │    0x00049240 73686f75 6c642062 65202564 0a000000 should be %d....
│ │ │ │    0x00049250 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00049260 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00049260 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00049270 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x00049280 2f73696d 34636f72 652f676c 696d6d65 /sim4core/glimme
│ │ │ │    0x00049290 7253706c 6963652e 43000000 00000000 rSplice.C.......
│ │ │ │    0x000492a0 4552524f 52207265 6164696e 67206963 ERROR reading ic
│ │ │ │    0x000492b0 6d206e6f 6465203d 20256420 20706572 m node = %d  per
│ │ │ │    0x000492c0 696f6420 3d202564 0a000000 00000000 iod = %d........
│ │ │ │    0x000492d0 4552524f 52207265 6164696e 67206d75 ERROR reading mu
│ │ │ │ @@ -873,15 +873,15 @@
│ │ │ │    0x00049660 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x00049670 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x00049680 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x00049690 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x000496a0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x000496b0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x000496c0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x000496d0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x000496d0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x000496e0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x000496f0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x00049700 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x00049710 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x00049720 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x00049730 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x00049740 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ │ @@ -995,15 +995,15 @@
│ │ │ │    0x00049e00 03dcfeff 03dcfeff 03dcfeff 03dcfeff ................
│ │ │ │    0x00049e10 03dcfeff 05e0feff 03dcfeff 11e0feff ................
│ │ │ │    0x00049e20 03dcfeff 1de0feff 73657143 61636865 ........seqCache
│ │ │ │    0x00049e30 3a3a6c6f 6164416c 6c536571 75656e63 ::loadAllSequenc
│ │ │ │    0x00049e40 65732829 2d2d2046 61696c65 6420746f es()-- Failed to
│ │ │ │    0x00049e50 206c6f61 64206969 64202575 2e0a0000  load iid %u....
│ │ │ │    0x00049e60 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x00049e70 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x00049e70 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x00049e80 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x00049e90 73657146 6163746f 72792e43 00000000 seqFactory.C....
│ │ │ │    0x00049ea0 73657146 6163746f 72793a3a 72656769 seqFactory::regi
│ │ │ │    0x00049eb0 73746572 46696c65 28292d2d 2020576f sterFile()--  Wo
│ │ │ │    0x00049ec0 77212020 596f7520 72656769 73746572 w!  You register
│ │ │ │    0x00049ed0 6564206c 6f747320 6f662066 696c6573 ed lots of files
│ │ │ │    0x00049ee0 2120204e 6f772066 69782025 73206174 !  Now fix %s at
│ │ │ │ @@ -1084,15 +1084,15 @@
│ │ │ │    0x0004a390 28292d2d 20455252 4f522120 20557365 ()-- ERROR!  Use
│ │ │ │    0x0004a3a0 6420666f 72207261 6e646f6d 20616363 d for random acc
│ │ │ │    0x0004a3b0 6573732e 0a000000 76697274 75616c20 ess.....virtual 
│ │ │ │    0x0004a3c0 75696e74 33322066 61737461 53746469 uint32 fastaStdi
│ │ │ │    0x0004a3d0 6e3a3a66 696e6428 636f6e73 74206368 n::find(const ch
│ │ │ │    0x0004a3e0 61722a29 00000000 2f627569 6c642f6b ar*)..../build/k
│ │ │ │    0x0004a3f0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0004a400 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0004a400 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0004a410 2f6c6962 7365712f 66617374 61537464 /libseq/fastaStd
│ │ │ │    0x0004a420 696e2e43 00000000 66617374 61537464 in.C....fastaStd
│ │ │ │    0x0004a430 696e3a3a 67657453 65717565 6e636528 in::getSequence(
│ │ │ │    0x0004a440 70617274 292d2d20 4552524f 52212020 part)-- ERROR!  
│ │ │ │    0x0004a450 55736564 20666f72 2072616e 646f6d20 Used for random 
│ │ │ │    0x0004a460 61636365 73732e0a 00000000 00000000 access..........
│ │ │ │    0x0004a470 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │ @@ -1163,15 +1163,15 @@
│ │ │ │    0x0004a880 76697274 75616c20 626f6f6c 20666173 virtual bool fas
│ │ │ │    0x0004a890 74714669 6c653a3a 67657453 65717565 tqFile::getSeque
│ │ │ │    0x0004a8a0 6e636528 75696e74 33322c20 63686172 nce(uint32, char
│ │ │ │    0x0004a8b0 2a262c20 75696e74 3332262c 2075696e *&, uint32&, uin
│ │ │ │    0x0004a8c0 74333226 2c206368 61722a26 2c207569 t32&, char*&, ui
│ │ │ │    0x0004a8d0 6e743332 262c2075 696e7433 32262900 nt32&, uint32&).
│ │ │ │    0x0004a8e0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0004a8f0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0004a8f0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0004a900 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x0004a910 66617374 7146696c 652e4300 00000000 fastqFile.C.....
│ │ │ │    0x0004a920 285f7262 2d3e656f 66282920 3d3d2074 (_rb->eof() == t
│ │ │ │    0x0004a930 72756529 207c7c20 2878203d 3d20272b rue) || (x == '+
│ │ │ │    0x0004a940 27290000 00000000 66617374 7146696c ')......fastqFil
│ │ │ │    0x0004a950 653a3a63 6f6e7374 72756374 496e6465 e::constructInde
│ │ │ │    0x0004a960 7828292d 2d207374 6174206f 66206669 x()-- stat of fi
│ │ │ │ @@ -1216,15 +1216,15 @@
│ │ │ │    0x0004abd0 696e3a3a 66696e64 28292d2d 20455252 in::find()-- ERR
│ │ │ │    0x0004abe0 4f522120 20557365 6420666f 72207261 OR!  Used for ra
│ │ │ │    0x0004abf0 6e646f6d 20616363 6573732e 0a000000 ndom access.....
│ │ │ │    0x0004ac00 76697274 75616c20 75696e74 33322066 virtual uint32 f
│ │ │ │    0x0004ac10 61737471 53746469 6e3a3a66 696e6428 astqStdin::find(
│ │ │ │    0x0004ac20 636f6e73 74206368 61722a29 00000000 const char*)....
│ │ │ │    0x0004ac30 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0004ac40 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0004ac40 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0004ac50 30332b72 32303133 2f6c6962 7365712f 03+r2013/libseq/
│ │ │ │    0x0004ac60 66617374 71537464 696e2e43 00000000 fastqStdin.C....
│ │ │ │    0x0004ac70 66617374 71537464 696e3a3a 67657453 fastqStdin::getS
│ │ │ │    0x0004ac80 65717565 6e636528 70617274 292d2d20 equence(part)-- 
│ │ │ │    0x0004ac90 4552524f 52212020 55736564 20666f72 ERROR!  Used for
│ │ │ │    0x0004aca0 2072616e 646f6d20 61636365 73732e0a  random access..
│ │ │ │    0x0004acb0 00000000 00000000 76697274 75616c20 ........virtual 
│ │ │ │ @@ -1288,15 +1288,15 @@
│ │ │ │    0x0004b050 626f6f6c 20736571 53746f72 653a3a67 bool seqStore::g
│ │ │ │    0x0004b060 65745365 7175656e 63652875 696e7433 etSequence(uint3
│ │ │ │    0x0004b070 322c2063 6861722a 262c2075 696e7433 2, char*&, uint3
│ │ │ │    0x0004b080 32262c20 75696e74 3332262c 20636861 2&, uint32&, cha
│ │ │ │    0x0004b090 722a262c 2075696e 74333226 2c207569 r*&, uint32&, ui
│ │ │ │    0x0004b0a0 6e743332 26290000 2f627569 6c642f6b nt32&)../build/k
│ │ │ │    0x0004b0b0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0004b0c0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0004b0c0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0004b0d0 2f6c6962 7365712f 73657153 746f7265 /libseq/seqStore
│ │ │ │    0x0004b0e0 2e430000 00000000 5f627066 2d3e7465 .C......_bpf->te
│ │ │ │    0x0004b0f0 6c6c2829 203d3d20 5f626c6f 636b5b62 ll() == _block[b
│ │ │ │    0x0004b100 6c6f636b 5d2e5f62 7066202a 20320000 lock]._bpf * 2..
│ │ │ │    0x0004b110 73657153 746f7265 3a3a6765 74536571 seqStore::getSeq
│ │ │ │    0x0004b120 75656e63 65287061 7274292d 2d202069 uence(part)--  i
│ │ │ │    0x0004b130 69642025 75206d6f 72652074 68616e20 id %u more than 
│ │ │ │ @@ -1321,15 +1321,15 @@
│ │ │ │    0x0004b260 20736571 75656e63 6573202d 2d202535  sequences -- %5
│ │ │ │    0x0004b270 2e306620 73657175 656e6365 732f7365 .0f sequences/se
│ │ │ │    0x0004b280 636f6e64 0d000000 766f6964 20626974 cond....void bit
│ │ │ │    0x0004b290 5061636b 65644669 6c653a3a 70757442 PackedFile::putB
│ │ │ │    0x0004b2a0 69747328 75696e74 36342c20 75696e74 its(uint64, uint
│ │ │ │    0x0004b2b0 33322900 00000000 2f627569 6c642f6b 32)...../build/k
│ │ │ │    0x0004b2c0 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0004b2d0 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0004b2d0 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0004b2e0 2f6c6962 7574696c 2f626974 5061636b /libutil/bitPack
│ │ │ │    0x0004b2f0 65644669 6c652e48 00000000 00000000 edFile.H........
│ │ │ │    0x0004b300 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ │    0x0004b310 6528292d 2d202046 61696c65 6420746f e()--  Failed to
│ │ │ │    0x0004b320 2072656f 70656e20 27257327 20746f20  reopen '%s' to 
│ │ │ │    0x0004b330 77726974 65206461 74613a20 25730a00 write data: %s..
│ │ │ │    0x0004b340 636f6e73 74727563 74536571 53746f72 constructSeqStor
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 39613439 31353138 38336434 62313436 9a49151883d4b146
│ │ │ │ -  0x00000010 64353538 38376432 32383133 64353530 d55887d22813d550
│ │ │ │ -  0x00000020 36303462 36302e64 65627567 00000000 604b60.debug....
│ │ │ │ -  0x00000030 f6e4b867                            ...g
│ │ │ │ +  0x00000000 32366361 38343765 30383836 38616639 26ca847e08868af9
│ │ │ │ +  0x00000010 62376435 64336138 64626132 39646538 b7d5d3a8dba29de8
│ │ │ │ +  0x00000020 63663866 63392e64 65627567 00000000 cf8fc9.debug....
│ │ │ │ +  0x00000030 6222c61c                            b"..
│ │ ├── ./usr/bin/sortPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 2507c003514e8279219866e32de38127ab3004fc
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 1a6cb97b27431659d802995a26d1dfb40afea819
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -110,15 +110,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -146,15 +146,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -238,15 +238,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -07c003514e8279219866e32de38127ab3004fc.debug
│ │ │ │ +6cb97b27431659d802995a26d1dfb40afea819.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -88,15 +88,15 @@
│ │ │ │    0x0000c550 0a00203f 3f00203d 3d00202d 2d00203c .. ??. ==. --. <
│ │ │ │    0x0000c560 2d00202d 3e00554e 4b4e4f57 4e006572 -. ->.UNKNOWN.er
│ │ │ │    0x0000c570 726f7200 61626f72 74656400 696e7472 ror.aborted.intr
│ │ │ │    0x0000c580 61637461 626c6500 756e6b6e 6f776e00 actable.unknown.
│ │ │ │    0x0000c590 72657665 72736500 666f7277 61726400 reverse.forward.
│ │ │ │    0x0000c5a0 636f6d70 6c656d65 6e740000 00000000 complement......
│ │ │ │    0x0000c5b0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000c5c0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000c5c0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000c5d0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000c5e0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000c5f0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000c600 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000c610 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000c620 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000c630 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -221,15 +221,15 @@
│ │ │ │    0x0000cda0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000cdb0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000cdc0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000cdd0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000cde0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000cdf0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000ce00 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000ce10 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000ce10 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000ce20 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000ce30 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000ce40 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000ce50 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000ce60 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000ce70 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000ce80 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 30376330 30333531 34653832 37393231 07c003514e827921
│ │ │ │ -  0x00000010 39383636 65333264 65333831 32376162 9866e32de38127ab
│ │ │ │ -  0x00000020 33303034 66632e64 65627567 00000000 3004fc.debug....
│ │ │ │ -  0x00000030 bb51dedd                            .Q..
│ │ │ │ +  0x00000000 36636239 37623237 34333136 35396438 6cb97b27431659d8
│ │ │ │ +  0x00000010 30323939 35613236 64316466 62343061 02995a26d1dfb40a
│ │ │ │ +  0x00000020 66656138 31392e64 65627567 00000000 fea819.debug....
│ │ │ │ +  0x00000030 2404062c                            $..,
│ │ ├── ./usr/bin/summarizePolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 790cbe79024f73f73a588285abd0196767b6b4cb
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: bbf3ded957bd3a6346bf291eabc2755de30ef855
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -112,15 +112,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -131,15 +131,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -212,15 +212,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -0cbe79024f73f73a588285abd0196767b6b4cb.debug
│ │ │ │ +f3ded957bd3a6346bf291eabc2755de30ef855.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -110,15 +110,15 @@
│ │ │ │    0x0000b6b0 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000b6c0 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000b6d0 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000b6e0 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000b6f0 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000b700 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000b710 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000b720 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000b720 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000b730 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000b740 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000b750 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000b760 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000b770 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000b780 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000b790 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -181,15 +181,15 @@
│ │ │ │    0x0000bb20 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000bb30 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000bb40 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000bb50 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000bb60 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000bb70 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000bb80 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000bb90 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000bb90 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000bba0 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000bbb0 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000bbc0 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000bbd0 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000bbe0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000bbf0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000bc00 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 30636265 37393032 34663733 66373361 0cbe79024f73f73a
│ │ │ │ -  0x00000010 35383832 38356162 64303139 36373637 588285abd0196767
│ │ │ │ -  0x00000020 62366234 63622e64 65627567 00000000 b6b4cb.debug....
│ │ │ │ -  0x00000030 cb893a17                            ..:.
│ │ │ │ +  0x00000000 66336465 64393537 62643361 36333436 f3ded957bd3a6346
│ │ │ │ +  0x00000010 62663239 31656162 63323735 35646533 bf291eabc2755de3
│ │ │ │ +  0x00000020 30656638 35352e64 65627567 00000000 0ef855.debug....
│ │ │ │ +  0x00000030 44b49a38                            D..8
│ │ ├── ./usr/bin/uniqPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 542ec04a5ccba2b2824e1652dcc74f3a16df8671
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: 02c2b12ce51a4b320291ac7eaa505fc37b57f991
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -81,15 +81,15 @@
│ │ │ │  char* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -117,15 +117,15 @@
│ │ │ │  Csim4end
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -198,15 +198,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................01234...........................................................................................................................10324...........................................................................................................................23014...........................................................................................................................32104...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -2ec04a5ccba2b2824e1652dcc74f3a16df8671.debug
│ │ │ │ +c2b12ce51a4b320291ac7eaa505fc37b57f991.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -23,15 +23,15 @@
│ │ │ │    0x0000a140 00203f3f 00203d3d 00202d2d 00203c2d . ??. ==. --. <-
│ │ │ │    0x0000a150 00202d3e 00554e4b 4e4f574e 00657272 . ->.UNKNOWN.err
│ │ │ │    0x0000a160 6f720061 626f7274 65640069 6e747261 or.aborted.intra
│ │ │ │    0x0000a170 63746162 6c650075 6e6b6e6f 776e0072 ctable.unknown.r
│ │ │ │    0x0000a180 65766572 73650066 6f727761 72640063 everse.forward.c
│ │ │ │    0x0000a190 6f6d706c 656d656e 74000000 00000000 omplement.......
│ │ │ │    0x0000a1a0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000a1b0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000a1b0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000a1c0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000a1d0 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000a1e0 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000a1f0 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000a200 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000a210 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000a220 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -157,15 +157,15 @@
│ │ │ │    0x0000a9a0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000a9b0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000a9c0 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000a9d0 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000a9e0 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000a9f0 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000aa00 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000aa10 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000aa10 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000aa20 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000aa30 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000aa40 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000aa50 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000aa60 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000aa70 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000aa80 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 32656330 34613563 63626132 62323832 2ec04a5ccba2b282
│ │ │ │ -  0x00000010 34653136 35326463 63373466 33613136 4e1652dcc74f3a16
│ │ │ │ -  0x00000020 64663836 37312e64 65627567 00000000 df8671.debug....
│ │ │ │ -  0x00000030 8df049fe                            ..I.
│ │ │ │ +  0x00000000 63326231 32636535 31613462 33323032 c2b12ce51a4b3202
│ │ │ │ +  0x00000010 39316163 37656161 35303566 63333762 91ac7eaa505fc37b
│ │ │ │ +  0x00000020 35376639 39312e64 65627567 00000000 57f991.debug....
│ │ │ │ +  0x00000030 fce19381                            ....
│ │ ├── ./usr/bin/vennPolishes
│ │ │ ├── readelf --wide --notes {}
│ │ │ │ @@ -1,8 +1,8 @@
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.gnu.build-id
│ │ │ │    Owner                Data size 	Description
│ │ │ │ -  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: aa4a1a1cb20021b0e6b8ceb603d66c04a84c74e0
│ │ │ │ +  GNU                  0x00000014	NT_GNU_BUILD_ID (unique build ID bitstring)	    Build ID: ece9cbb2b4c9fb76ecdb60b2adac6eb7b0ac507a
│ │ │ │  
│ │ │ │  Displaying notes found in: .note.ABI-tag
│ │ │ │    Owner                Data size 	Description
│ │ │ │    GNU                  0x00000010	NT_GNU_ABI_TAG (ABI version tag)	    OS: Linux, ABI: 3.2.0
│ │ │ ├── strings --all --bytes=8 {}
│ │ │ │ @@ -112,15 +112,15 @@
│ │ │ │  Cchar* encodeGap(char*, char*)
│ │ │ │  lenref == lentgt
│ │ │ │  comment=%s
│ │ │ │  %u-%u (%u-%u) <%u-%u-%u>%s
│ │ │ │  ;intron=%s
│ │ │ │  intractable
│ │ │ │  complement
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C
│ │ │ │  sim4reader: Unknown matchOrientation '%u' in printPolish()
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolish()
│ │ │ │  sim4begin
│ │ │ │  %u[%u-%u-%u] %u[%u-%u] <%u-%u-%u-%s-%s>
│ │ │ │  sim4reader: Unknown strandOrientation '%u' in printPolishGFF3()
│ │ │ │  %u:%s	sim4db	mRNA	%u	%u	%u	%c	.	
│ │ │ │  ID=sim4db%u;Name=%u:%s;Target=%u:%s %u %u %c;
│ │ │ │ @@ -131,15 +131,15 @@
│ │ │ │  s4p_polishToString()-- unknown style='%d'
│ │ │ │  	sim4db	mRNA
│ │ │ │  	sim4db	exon	
│ │ │ │  sim4reader: Got '%s', expecting 'sim4begin' at byte %lu
│ │ │ │  ERROR: too many lines, lazy programmer.
│ │ │ │  sim4reader: Got '%s', expecting GFF3 mRNA line at byte %lu
│ │ │ │  void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)
│ │ │ │ -/build/kmer-Dir4X3/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │ +/build/kmer-Dir4X3/kmer-0-20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()-- Invalid sim4db format, got '%s' instead of sim4begin.  Cannot convert.
│ │ │ │  %u[%u %u %u] %u[%u %u] <%u %u %u %s %s>
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  byte %u: '%s'
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  Expecting description line, found %d tokens instead of 12.
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown match orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  unknown strand orientation
│ │ │ │  sim4polish::s4p_linesToPolishS4DB()--  WARNING: found ZERO exons?
│ │ │ │ @@ -212,15 +212,15 @@
│ │ │ │  readBuffer()-- '%s' couldn't seek to position %ld: %s
│ │ │ │  readBuffer()-- couldn't read %lu bytes from '%s': n%s
│ │ │ │  ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................catgn............14044434444444444442444444......14044434444444444442444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................gtacn............24344404444444444441444444......24344404444444444441444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................acgtn............04144424444444444443444444......04144424444444444443444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................tgcan............34244414444444444440444444......34244414444444444440444444......................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3............................................................................0.1...2......4.....3............0.1...2......4.....3...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
│ │ │ │  ????????????????????????????????????????????????0123?????????????TVGH??CD??M?KN???YWAABS?R???????tvgh??cd??m?kn???ywaabs?r??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????0123????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACGT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
│ │ │ │   !"#$%&'()*+,-./0123456789:;<=>?@abcdefghijklmnopqrstuvwxyz[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
│ │ │ │  /usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug
│ │ │ │ -4a1a1cb20021b0e6b8ceb603d66c04a84c74e0.debug
│ │ │ │ +e9cbb2b4c9fb76ecdb60b2adac6eb7b0ac507a.debug
│ │ │ │  .shstrtab
│ │ │ │  .note.gnu.build-id
│ │ │ │  .note.ABI-tag
│ │ │ │  .gnu.hash
│ │ │ │  .gnu.version
│ │ │ │  .gnu.version_r
│ │ │ │  .rela.dyn
│ │ │ ├── readelf --wide --decompress --hex-dump=.rodata {}
│ │ │ │ @@ -138,15 +138,15 @@
│ │ │ │    0x0000a870 203f3f00 203d3d00 202d2d00 203c2d00  ??. ==. --. <-.
│ │ │ │    0x0000a880 202d3e00 554e4b4e 4f574e00 6572726f  ->.UNKNOWN.erro
│ │ │ │    0x0000a890 72006162 6f727465 6400696e 74726163 r.aborted.intrac
│ │ │ │    0x0000a8a0 7461626c 6500756e 6b6e6f77 6e007265 table.unknown.re
│ │ │ │    0x0000a8b0 76657273 6500666f 72776172 6400636f verse.forward.co
│ │ │ │    0x0000a8c0 6d706c65 6d656e74 00000000 00000000 mplement........
│ │ │ │    0x0000a8d0 2f627569 6c642f6b 6d65722d 44697234 /build/kmer-Dir4
│ │ │ │ -  0x0000a8e0 58332f6b 6d65722d 307e3230 31353039 X3/kmer-0~201509
│ │ │ │ +  0x0000a8e0 58332f6b 6d65722d 302d3230 31353039 X3/kmer-0-201509
│ │ │ │    0x0000a8f0 30332b72 32303133 2f6c6962 73696d34 03+r2013/libsim4
│ │ │ │    0x0000a900 2f73696d 34706f6c 6973682f 73696d34 /sim4polish/sim4
│ │ │ │    0x0000a910 706f6c69 73682d70 6f6c6973 68746f73 polish-polishtos
│ │ │ │    0x0000a920 7472696e 672e4300 73696d34 72656164 tring.C.sim4read
│ │ │ │    0x0000a930 65723a20 556e6b6e 6f776e20 6d617463 er: Unknown matc
│ │ │ │    0x0000a940 684f7269 656e7461 74696f6e 20272575 hOrientation '%u
│ │ │ │    0x0000a950 2720696e 20707269 6e74506f 6c697368 ' in printPolish
│ │ │ │ @@ -209,15 +209,15 @@
│ │ │ │    0x0000ace0 74206279 74652025 6c750a00 00000000 t byte %lu......
│ │ │ │    0x0000acf0 766f6964 2073696d 34706f6c 6973683a void sim4polish:
│ │ │ │    0x0000ad00 3a733470 5f6c696e 6573546f 506f6c69 :s4p_linesToPoli
│ │ │ │    0x0000ad10 73685334 44422875 696e7433 322c2075 shS4DB(uint32, u
│ │ │ │    0x0000ad20 696e7433 322c2063 6861722a 2a2c2075 int32, char**, u
│ │ │ │    0x0000ad30 696e7433 322a2900 2f627569 6c642f6b int32*)./build/k
│ │ │ │    0x0000ad40 6d65722d 44697234 58332f6b 6d65722d mer-Dir4X3/kmer-
│ │ │ │ -  0x0000ad50 307e3230 31353039 30332b72 32303133 0~20150903+r2013
│ │ │ │ +  0x0000ad50 302d3230 31353039 30332b72 32303133 0-20150903+r2013
│ │ │ │    0x0000ad60 2f6c6962 73696d34 2f73696d 34706f6c /libsim4/sim4pol
│ │ │ │    0x0000ad70 6973682f 73696d34 706f6c69 73682d73 ish/sim4polish-s
│ │ │ │    0x0000ad80 7472696e 67746f70 6f6c6973 682e4300 tringtopolish.C.
│ │ │ │    0x0000ad90 73696d34 706f6c69 73683a3a 7334705f sim4polish::s4p_
│ │ │ │    0x0000ada0 6c696e65 73546f50 6f6c6973 68533444 linesToPolishS4D
│ │ │ │    0x0000adb0 4228292d 2d20496e 76616c69 64207369 B()-- Invalid si
│ │ │ │    0x0000adc0 6d346462 20666f72 6d61742c 20676f74 m4db format, got
│ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {}
│ │ │ │ @@ -1,7 +1,7 @@
│ │ │ │  
│ │ │ │  Hex dump of section '.gnu_debuglink':
│ │ │ │ -  0x00000000 34613161 31636232 30303231 62306536 4a1a1cb20021b0e6
│ │ │ │ -  0x00000010 62386365 62363033 64363663 30346138 b8ceb603d66c04a8
│ │ │ │ -  0x00000020 34633734 65302e64 65627567 00000000 4c74e0.debug....
│ │ │ │ -  0x00000030 e2e6583a                            ..X:
│ │ │ │ +  0x00000000 65396362 62326234 63396662 37366563 e9cbb2b4c9fb76ec
│ │ │ │ +  0x00000010 64623630 62326164 61633665 62376230 db60b2adac6eb7b0
│ │ │ │ +  0x00000020 61633530 37612e64 65627567 00000000 ac507a.debug....
│ │ │ │ +  0x00000030 5dffe367                            ]..g