Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/staden-io-lib/staden-io-lib_1.14.13-4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/staden-io-lib-1.14.13-4lr29elf2/staden-io-lib_1.14.13-4_amd64.buildinfo Get source package info: staden-io-lib=1.14.13-4 Source URL: http://snapshot.notset.fr/mr/package/staden-io-lib/1.14.13-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 apt=2.1.7 autoconf=2.69-11.1 automake=1:1.16.2-3 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.35-1 binutils-common=2.35-1 binutils-x86-64-linux-gnu=2.35-1 bsdextrautils=2.36-1 bsdutils=1:2.36-1 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-3 cpp=4:10.1.0-1 cpp-10=10.2.0-3 d-shlibs=0.93 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2 debian-archive-keyring=2019.1 debianutils=4.11 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 g++=4:10.1.0-1 g++-10=10.2.0-3 gcc=4:10.1.0-1 gcc-10=10.2.0-3 gcc-10-base=10.2.0-3 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gpgv=2.2.20-1 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libapt-pkg6.0=2.1.7 libarchive-zip-perl=1.68-1 libasan6=10.2.0-3 libatomic1=10.2.0-3 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.35-1 libblkid1=2.36-1 libbrotli1=1.0.7-7 libbz2-1.0=1.0.8-4 libc-bin=2.31-2 libc-dev-bin=2.31-2 libc6=2.31-2 libc6-dev=2.31-2 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-3 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.35-1 libctf0=2.35-1 libcurl3-gnutls=7.68.0-1+b1 libcurl4-gnutls-dev=7.68.0-1+b1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.253 libdebhelper-perl=13.2 libdpkg-perl=1.20.5 libelf1=0.180-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-3 libgcc-s1=10.2.0-3 libgcrypt20=1.8.6-2 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.4-1 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.14-2+b1 libgomp1=10.2.0-3 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhogweed6=3.6-2 libhtscodecs-dev=0.5-3 libhtscodecs2=0.5-3 libicu67=67.1-3 libidn2-0=2.3.0-1 libisl22=0.22.1-1 libitm1=10.2.0-3 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.50+dfsg-1+b1 libldap-common=2.4.50+dfsg-1 liblsan0=10.2.0-3 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-1 libmpc3=1.1.0-1 libmpfr6=4.1.0-3 libnettle8=3.6-2 libnghttp2-14=1.41.0-2 libp11-kit0=0.23.20-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.2-2 libpsl5=0.21.0-1.1 libquadmath0=10.2.0-3 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.3-1+b1 libselinux1=3.1-2 libsemanage-common=3.1-1 libsemanage1=3.1-1 libsepol1=3.1-1 libsigsegv2=2.12-2 libsmartcols1=2.36-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1g-1 libstdc++-10-dev=10.2.0-3 libstdc++6=10.2.0-3 libsub-override-perl=0.09-2 libsystemd0=245.6-3 libtasn1-6=4.16.0-2 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10.2.0-3 libubsan1=10.2.0-3 libuchardet0=0.0.7-1 libudev1=245.6-3 libunistring2=0.9.10-4 libuuid1=2.36-1 libxml2=2.9.10+dfsg-5+b1 libzstd1=1.4.5+dfsg-3 linux-libc-dev=5.7.10-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2-1 ncurses-bin=6.2-1 passwd=1:4.8.1-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 util-linux=2.36-1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200727T204945Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d staden-io-lib=1.14.13-4 && mkdir -p /build/staden-io-lib-wkrazz && dpkg-source --no-check -x /*.dsc /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13 && chown -R builduser:builduser /build/staden-io-lib-wkrazz" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1595932940" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/staden-io-lib-wkrazz /tmp/staden-io-lib-1.14.13-4lr29elf2 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200727T204945Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.x4_2i35ehP as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.x4_2i35ehP Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200727T204945Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200727T204945Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (518 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4578 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-2) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200727T204945Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.x4_2i35ehP Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200727T204945Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1162 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.x4_2i35ehP I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d staden-io-lib=1.14.13-4 && mkdir -p /build/staden-io-lib-wkrazz && dpkg-source --no-check -x /*.dsc /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13 && chown -R builduser:builduser /build/staden-io-lib-wkrazz"' exec /tmp/mmdebstrap.x4_2i35ehP Reading package lists... NOTICE: 'staden-io-lib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/staden-io-lib.git Please use: git clone https://salsa.debian.org/med-team/staden-io-lib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3400 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main staden-io-lib 1.14.13-4 (dsc) [2469 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main staden-io-lib 1.14.13-4 (tar) [3379 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main staden-io-lib 1.14.13-4 (diff) [18.4 kB] Fetched 3400 kB in 3s (1215 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'staden-io-lib_1.14.13-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting staden-io-lib in /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13 dpkg-source: info: unpacking staden-io-lib_1.14.13.orig.tar.gz dpkg-source: info: unpacking staden-io-lib_1.14.13-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 32-bit.patch dpkg-source: info: applying pathmax.patch dpkg-source: info: applying fix_fseeko.patch dpkg-source: info: applying spelling dpkg-source: info: applying usedebianhtscodecs.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1595932940" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.x4_2i35ehP dpkg-buildpackage: info: source package staden-io-lib dpkg-buildpackage: info: source version 1.14.13-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' dh_auto_clean rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam rm -f config.sub config.guess ## ## Try to verify correct ABI version right in the beginning ## Strangely enough d-shlibmove fails in detecting it in this package ## Since upstream build system creates libstaden-read.so.11.1.0 this code is not ## activated but it should be considered in case of future problems with ABI version ## #UPSTREAMABI=`grep ^VERS_CURRENT configure.in | sed 's/^VERS_CURRENT[[:space:]]*=\([0-9]\+\)[[:space:]]*/\1/'` ; \ #DEBABI=`grep '^Package: libstaden-read[0-9]\+' debian/control | sed 's/Package: libstaden-read\([0-9]\+\)/\1/'` ; \ #if [ ${UPSTREAMABI} -ne ${DEBABI} ] ; then \ # echo "Upstream has bumped ABI to ${UPSTREAMABI} but Debian is using libstaden-read${DEBABI} (see bug #710225)" ; \ # exit 1 ; \ #fi make[1]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -O--no-parallel libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:79: installing './compile' configure.ac:81: installing './config.guess' configure.ac:81: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.68.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... no checking for lzma_easy_buffer_encode in -llzma... no checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking stdio_ext.h usability... yes checking stdio_ext.h presence... yes checking for stdio_ext.h... yes checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... yes checking for fileno... yes checking for fstat... yes checking for mallopt... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... (cached) yes checking for library containing pthread_join... -lpthread checking for library containing cos... -lm checking for strdup... yes checking for fsync... yes checking that generated files are newer than configure... done === configuring in htscodecs (/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/htscodecs) configure: WARNING: no configuration information is in htscodecs configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands make[1]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' dh_auto_build -a -O--no-parallel make -j1 make[1]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make all-recursive make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' Making all in io_lib make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOPlain.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOPlain.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c read_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-read_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c write_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-write_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c write_scf.c -o libstaden_read_la-write_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c sff.c -fPIC -DPIC -o .libs/libstaden_read_la-sff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c sff.c -o libstaden_read_la-sff.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c srf.c -fPIC -DPIC -o .libs/libstaden_read_la-srf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time 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-D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o In file included from /usr/include/string.h:495, from bam.c:44: In function ‘memcpy’, inlined from ‘bam_cigar2tag’ at bam.c:1794:5, inlined from ‘bam_put_seq’ at bam.c:3891:10: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:10: warning: writing 8 bytes into a region of size 1 [-Wstringop-overflow=] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bam.c:59: bam.c: In function ‘bam_put_seq’: ../io_lib/bam.h:102:19: note: at offset 0 to object ‘data’ with size 1 declared here 102 | unsigned char data; /* unknown size */ | ^~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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-Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 15:0:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -lpthread libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so -lhtscodecs -lm -lpthread -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.0 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.0" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.0" "libstaden-read.so") libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' Making all in progs make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o convert_trace.o convert_trace.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeSCF.o makeSCF.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_seq.o extract_seq.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_qual.o extract_qual.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_fastq.o extract_fastq.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index_tar.o index_tar.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o index_tar index_tar.o -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o index_tar index_tar.o -lm -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scf_dump.o scf_dump.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scf_info.o scf_info.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 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cram_dump.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_index.o cram_index.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scramble.o scramble.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_merge.o scram_merge.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_pileup.o scram_pileup.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_flagstat.o scram_flagstat.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_test.o scram_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_size.o cram_size.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_filter.o cram_filter.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' Making all in tests make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_io_test.o cram_io_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -pthread make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[1]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' dh_auto_test -a -O--no-parallel make -j1 check VERBOSE=1 make[1]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' Making check in io_lib make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' Making check in progs make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' Making check in tests make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make check-TESTS make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' PASS: srf2fasta.test PASS: srf2fastq.test PASS: srf_info.test Reading archive ./data/both.srf. PASS: srf_filter.test NB: The next line is expected to be an error message Malformed or missing index hash. Consider running srf_index_hash Nbuckets = 16 Nused = 20 Avg chain = 1.250000 Chain var.= 0.812500 %age full = 81.250000 max len = 3 Chain 0 = 3 Chain 1 = 8 Chain 2 = 3 Chain 3 = 2 PASS: srf_index.test Loading ce.fa Generating ce#sorted.sam Generating ce#unsorted.sam === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram.test === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt30.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt31.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x longref.sam test.out/longref.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -q test.out/longref.cram test.out/longref.sam ./compare_sam.pl test.out/longref.sam ./data/longref.sam PASS: scram_mt40.test Cannot open file test.out/aux#aux.full.cram PASS: cram_io.test === testing ./data/ce#5b_java.cram === ../progs/scramble -t4 -r ./data/ce.fa ./data/ce#5b_java.cram test.out/ce#5b_java.scramble.sam ./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam === testing ./data/tag_aux#aux_java.cram === ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram test.out/tag_aux#aux_java.scramble.sam ./compare_sam.pl ./data/tag_aux#aux_java.sam test.out/tag_aux#aux_java.scramble.sam === testing ./data/xx#large_aux_java.cram === ../progs/scramble -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram test.out/xx#large_aux_java.scramble.sam ./compare_sam.pl ./data/xx#large_aux_java.sam test.out/xx#large_aux_java.scramble.sam === testing ./data/9827_rand3.cram === ../progs/scramble -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram test.out/9827_rand3.scramble.sam ./data/9827_rand3.cram.fai: No such file or directory ./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam PASS: java.test =================== All 11 tests passed =================== make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[1]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--no-parallel dh_prep -a -O--no-parallel dh_auto_install -a -O--no-parallel make -j1 install DESTDIR=/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' Making install in io_lib make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.0 /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.0 libtool: install: (cd /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.0 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.0 libstaden-read.so.14; }; }) libtool: install: (cd /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.0 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.0 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: chmod 644 /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: ranlib /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib' Making install in progs make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/convert_trace /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/makeSCF /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_seq /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_qual /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_fastq /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_dump /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_info /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_update /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/get_comment /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_tar /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_extract /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_list /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/trace_dump /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_sff /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/append_sff /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/ztr_dump /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_dump_all /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_index_hash /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_linear /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_hash /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fastq /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fasta /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_filter /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_info /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_list /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_exp /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_dump /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_index /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scramble /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_merge /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_pileup /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_flagstat /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_test /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_size /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_filter /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_filter make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/progs' Making install in tests make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/tests' make[2]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[3]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin' /usr/bin/install -c io_lib-config '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/bin' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man1' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man3' /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man3' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man4' /usr/bin/install -c -m 644 man/man4/Read.4 '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man4' /bin/mkdir -p '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/include/io_lib' make[3]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[2]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' make[1]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' debian/rules override_dh_install-arch make[1]: Entering directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' dh_install -a mkdir -p /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/libstaden-read-dev/usr/bin mv /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/libstaden-read-dev/usr/bin # # Call d-shlibmove to comply with library packaging guide d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev "debian/tmp/usr/include" usr \ --override s/libhtscodecs2-dev/libhtscodecs-dev/ \ debian/tmp/usr/lib/*/libstaden-read.so Library package automatic movement utility --> libcurl4-gnutls-dev package exists. --> libhtscodecs-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstaden-read14/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14 debian/libstaden-read14/usr/lib/x86_64-linux-gnu mv /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.0 debian/libstaden-read14/usr/lib/x86_64-linux-gnu PKGDEV=libstaden-read-dev PKGSHL=libstaden-read14 install -d -m 755 debian/libstaden-read-dev/usr mv debian/tmp/usr/include debian/libstaden-read-dev/usr mkdir -p /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/libstaden-read-dev/usr/include/io_lib/ cp /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/io_lib_config.h /build/staden-io-lib-wkrazz/staden-io-lib-1.14.13/debian/libstaden-read-dev/usr/include/io_lib/ # make sure io_lib-config --libs will not return -pie (see #825461) find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \; make[1]: Leaving directory '/build/staden-io-lib-wkrazz/staden-io-lib-1.14.13' dh_installdocs -a -O--no-parallel dh_installchangelogs -a -O--no-parallel dh_installman -a -O--no-parallel dh_installsystemduser -a -O--no-parallel dh_perl -a -O--no-parallel dh_link -a -O--no-parallel dh_strip_nondeterminism -a -O--no-parallel dh_compress -a -O--no-parallel dh_fixperms -a -O--no-parallel dh_missing -a -O--no-parallel dh_dwz -a -a -O--no-parallel dh_strip -a -a -O--no-parallel dh_makeshlibs -a -a -O--no-parallel dh_shlibdeps -a -a -O--no-parallel dh_installdeb -a -O--no-parallel dh_gencontrol -a -O--no-parallel dh_md5sums -a -O--no-parallel dh_builddeb -a -O--no-parallel dpkg-deb: building package 'libstaden-read14-dbgsym' in '../libstaden-read14-dbgsym_1.14.13-4_amd64.deb'. dpkg-deb: building package 'staden-io-lib-utils' in '../staden-io-lib-utils_1.14.13-4_amd64.deb'. dpkg-deb: building package 'libstaden-read-dev' in '../libstaden-read-dev_1.14.13-4_amd64.deb'. dpkg-deb: building package 'staden-io-lib-utils-dbgsym' in '../staden-io-lib-utils-dbgsym_1.14.13-4_amd64.deb'. dpkg-deb: building package 'libstaden-read14' in '../libstaden-read14_1.14.13-4_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../staden-io-lib_1.14.13-4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/staden-io-lib-wkrazz /tmp/staden-io-lib-1.14.13-4lr29elf2 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.x4_2i35ehP... I: success in 971.0048 seconds md5: libstaden-read-dev_1.14.13-4_amd64.deb: OK md5: libstaden-read14-dbgsym_1.14.13-4_amd64.deb: OK md5: libstaden-read14_1.14.13-4_amd64.deb: OK md5: staden-io-lib-utils-dbgsym_1.14.13-4_amd64.deb: OK md5: staden-io-lib-utils_1.14.13-4_amd64.deb: OK sha1: libstaden-read-dev_1.14.13-4_amd64.deb: OK sha1: libstaden-read14-dbgsym_1.14.13-4_amd64.deb: OK sha1: libstaden-read14_1.14.13-4_amd64.deb: OK sha1: staden-io-lib-utils-dbgsym_1.14.13-4_amd64.deb: OK sha1: staden-io-lib-utils_1.14.13-4_amd64.deb: OK sha256: libstaden-read-dev_1.14.13-4_amd64.deb: OK sha256: libstaden-read14-dbgsym_1.14.13-4_amd64.deb: OK sha256: libstaden-read14_1.14.13-4_amd64.deb: OK sha256: staden-io-lib-utils-dbgsym_1.14.13-4_amd64.deb: OK sha256: staden-io-lib-utils_1.14.13-4_amd64.deb: OK Checksums: OK