Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/python-pysam/python-pysam_0.15.4+ds-3_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/python-pysam-0.15.4+ds-3wb95kbw1/python-pysam_0.15.4+ds-3_all.buildinfo Get source package info: python-pysam=0.15.4+ds-3 Source URL: http://snapshot.notset.fr/mr/package/python-pysam/0.15.4+ds-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 bcftools=1.10.2-2 binutils=2.34-6 binutils-common=2.34-6 binutils-x86-64-linux-gnu=2.34-6 bsdmainutils=11.1.2+b1 bsdutils=1:2.35.1-2 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-11 cython3=0.29.14-1 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13 debianutils=4.9.1 dh-autoreconf=19 dh-exec=0.23.2 dh-python=4.20200315 dh-strip-nondeterminism=1.8.0-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 file=1:5.38-4 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.3.0-11 gcc=4:9.2.1-3.1 gcc-10-base=10-20200502-1 gcc-9=9.3.0-11 gcc-9-base=9.3.0-11 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan5=9.3.0-11 libatomic1=10-20200502-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.34-6 libblkid1=2.35.1-2 libbrotli1=1.0.7-6.1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.30-7 libc-dev-bin=2.30-7 libc6=2.30-7 libc6-dev=2.30-7 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10-20200502-1 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=2.34-6 libctf0=2.34-6 libcurl3-gnutls=7.68.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.251 libdebhelper-perl=13 libdeflate0=1.5-3 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libexpat1-dev=2.2.9-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.0-1 libgcc-9-dev=9.3.0-11 libgcc-s1=10-20200502-1 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.2-1 libgmp10=2:6.2.0+dfsg-4 libgnutls30=3.6.13-2 libgomp1=10-20200502-1 libgpg-error0=1.37-1 libgssapi-krb5-2=1.17-7 libhogweed5=3.5.1+really3.5.1-2 libhts-dev=1.10.2-3 libhts3=1.10.2-3 libicu63=63.2-3 libidn2-0=2.3.0-1 libisl22=0.22.1-1 libitm1=10-20200502-1 libk5crypto3=1.17-7 libkeyutils1=1.6.1-2 libkrb5-3=1.17-7 libkrb5support0=1.17-7 libldap-2.4-2=2.4.50+dfsg-1 libldap-common=2.4.50+dfsg-1 liblsan0=10-20200502-1 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmount1=2.35.1-2 libmpc3=1.1.0-1 libmpdec2=2.4.2-3 libmpfr6=4.0.2-1 libncurses6=6.2-1 libncursesw6=6.2-1 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 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=2:8.39-12+b1 libperl5.30=5.30.0-10 libpipeline1=1.5.2-2 libpsl5=0.21.0-1 libpython3-all-dev=3.8.2-3 libpython3-dev=3.8.2-3 libpython3-stdlib=3.8.2-3 libpython3.8=3.8.3~rc1-1 libpython3.8-dev=3.8.3~rc1-1 libpython3.8-minimal=3.8.3~rc1-1 libpython3.8-stdlib=3.8.3~rc1-1 libquadmath0=10-20200502-1 libreadline8=8.0-4 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsmartcols1=2.35.1-2 libsqlite3-0=3.31.1-5 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1g-1 libstdc++-9-dev=9.3.0-11 libstdc++6=10-20200502-1 libsub-override-perl=0.09-2 libsystemd0=245.5-2 libtasn1-6=4.16.0-2 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10-20200502-1 libubsan1=10-20200502-1 libuchardet0=0.0.6-3 libudev1=245.5-2 libunistring2=0.9.10-2 libuuid1=2.35.1-2 libxml2=2.9.10+dfsg-5 linux-libc-dev=5.6.7-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-2 man-db=2.9.1-1 mawk=1.3.4.20200120-2 mime-support=3.64 ncurses-base=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.0-10 perl-base=5.30.0-10 perl-modules-5.30=5.30.0-10 po-debconf=1.0.21 python3=3.8.2-3 python3-all=3.8.2-3 python3-all-dev=3.8.2-3 python3-atomicwrites=1.3.0-1 python3-attr=19.3.0-4 python3-dev=3.8.2-3 python3-distutils=3.8.2-2 python3-importlib-metadata=1.6.0-1 python3-lib2to3=3.8.2-2 python3-minimal=3.8.2-3 python3-more-itertools=4.2.0-2 python3-packaging=20.3-1.2 python3-pkg-resources=46.1.3-1 python3-pluggy=0.13.0-4 python3-py=1.8.1-2 python3-pyparsing=2.4.7-1 python3-pytest=4.6.9-3 python3-setuptools=46.1.3-1 python3-six=1.14.0-3 python3-wcwidth=0.1.9+dfsg1-1 python3-zipp=1.0.0-2 python3.8=3.8.3~rc1-1 python3.8-dev=3.8.3~rc1-1 python3.8-minimal=3.8.3~rc1-1 readline-common=8.0-4 samtools=1.10-3 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tabix=1.10.2-3 tar=1.30+dfsg-7 util-linux=2.35.1-2 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/20200507T210258Z/ 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 python-pysam=0.15.4+ds-3 && mkdir -p /build/python-pysam-p3cTC6 && dpkg-source --no-check -x /*.dsc /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds && chown -R builduser:builduser /build/python-pysam-p3cTC6" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1588962455" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/python-pysam-p3cTC6 /tmp/python-pysam-0.15.4+ds-3wb95kbw1 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200507T210258Z 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.JMyu3HSbIG 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.JMyu3HSbIG Reading package lists... Building dependency tree... util-linux is already the newest version (2.35.1-2). 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/20200507T210258Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200507T210258Z 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 (1050 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 ... 4482 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 (2.30-7) ... 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/20200507T210258Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.JMyu3HSbIG Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200507T210258Z 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 22s (1028 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.JMyu3HSbIG I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d python-pysam=0.15.4+ds-3 && mkdir -p /build/python-pysam-p3cTC6 && dpkg-source --no-check -x /*.dsc /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds && chown -R builduser:builduser /build/python-pysam-p3cTC6"' exec /tmp/mmdebstrap.JMyu3HSbIG Reading package lists... NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pysam.git Please use: git clone https://salsa.debian.org/med-team/python-pysam.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1738 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main python-pysam 0.15.4+ds-3 (dsc) [2425 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main python-pysam 0.15.4+ds-3 (tar) [1362 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main python-pysam 0.15.4+ds-3 (diff) [374 kB] Fetched 1738 kB in 1s (1218 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'python-pysam_0.15.4+ds-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting python-pysam in /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds dpkg-source: info: unpacking python-pysam_0.15.4+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.15.4+ds-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying spelling dpkg-source: info: applying hts1.10 dpkg-source: info: applying samtools_v1.10_full dpkg-source: info: applying bcftools_v1.10_full dpkg-source: info: applying clean_less I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1588962455" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.JMyu3HSbIG dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.4+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/pysam_data' rm -fr *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds' dh_auto_clean I: pybuild base:217: python3.8 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-indep dh binary-indep --with python3 --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -i -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) copying pysam/libchtslib.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcutils.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/pysam_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/version.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools Fixing /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c cythoning pysam/libcutils.pyx to pysam/libcutils.c cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c cythoning pysam/libctabix.pyx to pysam/libctabix.c cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c cythoning pysam/libcbcf.pyx to pysam/libcbcf.c cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c cythoning pysam/libcvcf.pyx to pysam/libcvcf.c building 'pysam.libchtslib' extension creating build creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/pysam x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libchtslib.o build/temp.linux-x86_64-3.8/pysam/htslib_util.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-3.8/samtools creating build/temp.linux-x86_64-3.8/samtools/lz4 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-3.8/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/sam.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-3.8/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-3.8/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcsamtools.o build/temp.linux-x86_64-3.8/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-3.8/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-3.8/samtools/samtools.pysam.o build/temp.linux-x86_64-3.8/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.8/samtools/padding.c.pysam.o build/temp.linux-x86_64-3.8/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-3.8/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-3.8/samtools/tmp_file.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-3.8/samtools/stats.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-3.8/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-3.8/samtools/sam.c.pysam.o build/temp.linux-x86_64-3.8/samtools/coverage.c.pysam.o build/temp.linux-x86_64-3.8/samtools/faidx.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-3.8/samtools/sample.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.8/samtools/dict.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-3.8/samtools/phase.c.pysam.o build/temp.linux-x86_64-3.8/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-3.8/samtools/lz4/lz4.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-3.8/bcftools x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-3.8/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:694:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 694 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/vcf.h:41, from bcftools/vcfmerge.c.pysam.c:34: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-3.8/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcbcftools.o build/temp.linux-x86_64-3.8/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/cols.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/em.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/convert.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/version.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/bin.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/csq.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/main.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/filter.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/bcftools.pysam.o build/temp.linux-x86_64-3.8/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-3.8/bcftools/vcfstats.c.pysam.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcutils.c -o build/temp.linux-x86_64-3.8/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 511 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:5890:7: note: ‘__pyx_v_retval’ was declared here 5890 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/pysam_util.c -o build/temp.linux-x86_64-3.8/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcutils.o build/temp.linux-x86_64-3.8/pysam/pysam_util.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcsamtools.cpython-38-x86_64-linux-gnu -lcbcftools.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-3.8/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:29326:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 29326 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** {aka struct **} In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:604: /usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} 1709 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); | ~~~~~~~~~~~~~~~~~~~~~~^~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcalignmentfile.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-3.8/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcsamfile.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-3.8/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcalignedsegment.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libctabix.c -o build/temp.linux-x86_64-3.8/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); | ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) | ^~~~~~~~ pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libctabix.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-3.8/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcfaidx.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcbcf.c -o build/temp.linux-x86_64-3.8/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcbcf.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-3.8/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcbgzf.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libctabixproxies.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/samtools/lz4 -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/bcftools -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -I/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds -I/usr/include/python3.8 -c pysam/libcvcf.c -o build/temp.linux-x86_64-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/pysam/libcvcf.o -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2528:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2533:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2538:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/pysam_data' samtools faidx ex1.fa samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view -bS with_md.sam > with_md.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS tag_bug.sam > tag_bug.bam samtools view -bS ex9_fail.sam > ex9_fail.bam samtools view -bS ex10.sam > ex10.bam samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam samtools view -bS example_empty_header.sam > example_empty_header.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam samtools view -bS ex6.sam > ex6.bam samtools view -bS test_unaligned.sam > test_unaligned.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools view -bt tmp.list -o example_unmapped_reads_no_sq.bam example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view -bS ex4.sam > ex4.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index example_dash_in_chr.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index tag_bug.bam samtools index ex9_fail.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index ex5.bam samtools index example_reverse_complement.bam samtools index ex6.bam samtools index test_unaligned.bam samtools index ex_spliced.bam samtools index example_btag.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index ex4.bam samtools index ex8.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam grep "^@" ex2.sam | samtools view -Sb - > empty.bam samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam rm with_md.sam make[2]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/cbcf_data' bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < example_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf make[2]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/cbcf_data' export PYBUILD_TEST_ARGS='|| true' ; dh_auto_test I: pybuild base:217: cd /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build; python3.8 -m pytest || true ============================= test session starts ============================== platform linux -- Python 3.8.3rc1, pytest-4.6.9, py-1.8.1, pluggy-0.13.0 -- /usr/bin/python3.8 cachedir: .pytest_cache rootdir: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds, inifile: setup.cfg collecting ... collected 937 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp___enter___ak3rcpw0negative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works FAILED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected FAILED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works FAILED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected FAILED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_d0kfcs_5' /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_d0kfcs_5 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0vhtlus1' /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0vhtlus1 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_h3l3ux84 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_7zung2g_' /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_7zung2g_ PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_3j7wixdj' /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_3j7wixdj PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_b27vjwnk PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused FAILED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM FAILED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM [E::hts_open_format] Failed to open file "/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory FAILED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_bh0j7566tmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile FAILED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_ys8t4xiotmp_single.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_01fwfus0tmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile FAILED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader FAILED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header.bam' PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam' PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory FAILED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex2_truncated.bam' [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_26e3obl3tmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing FAILED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_eqvnnjzc.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =================================== FAILURES =================================== __________________ TestHeaderBAM.test_dictionary_access_works __________________ self = def test_dictionary_access_works(self): for key in self.header.keys(): > self.compare_headers({key: self.header[key]}, {key: self.samfile.header[key]}) tests/AlignmentFileHeader_test.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:143: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[155 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bS ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _______________ TestHeaderBAM.test_header_content_is_as_expected _______________ self = def test_header_content_is_as_expected(self): > self.compare_headers(self.header, self.samfile.header.to_dict()) tests/AlignmentFileHeader_test.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:143: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[155 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bS ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _________________ TestHeaderCRAM.test_dictionary_access_works __________________ self = def test_dictionary_access_works(self): for key in self.header.keys(): > self.compare_headers({key: self.header[key]}, {key: self.samfile.header[key]}) tests/AlignmentFileHeader_test.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:229: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[175 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] ______________ TestHeaderCRAM.test_header_content_is_as_expected _______________ self = def test_header_content_is_as_expected(self): > self.compare_headers(self.header, self.samfile.header.to_dict()) tests/AlignmentFileHeader_test.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:229: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[175 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _______________ BasicTestCRAMFromFetch.testPresentOptionalFields _______________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError _______________________ BasicTestCRAMFromFetch.testTags ________________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError _____________ BasicTestCRAMFromFilename.testPresentOptionalFields ______________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError ______________________ BasicTestCRAMFromFilename.testTags ______________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError _______________ BasicTestCRAMFromFile.testPresentOptionalFields ________________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError ________________________ BasicTestCRAMFromFile.testTags ________________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError ______________ BasicTestCRAMFromFileNo.testPresentOptionalFields _______________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError _______________________ BasicTestCRAMFromFileNo.testTags _______________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError ______________________________ TestIO.testBAM2SAM ______________________________ self = def testBAM2SAM(self): > self.checkEcho("ex2.bam", "ex2.sam", "tmp_ex2.sam", "rb", "wh") tests/AlignmentFile_test.py:497: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:447: in checkEcho self.assertTrue(checkf( E AssertionError: False is not true : files ex2.sam and tmp_ex2.sam are not the same ________________________ TestIO.testEmptyWithHeaderBAM _________________________ self = def testEmptyWithHeaderBAM(self): > self.assertRaises( ValueError, pysam.Samfile, os.path.join(BAM_DATADIR, "example_empty_with_header.bam"), "rb") tests/AlignmentFile_test.py:798: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E FileNotFoundError: [Errno 2] could not open alignment file `/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory pysam/libcalignmentfile.pyx:940: FileNotFoundError ______________________________ TestIO.testSAM2BAM ______________________________ self = def testSAM2BAM(self): > self.checkEcho("ex2.sam", "ex2.bam", "tmp_ex2.bam", "r", "wb", checkf=checkGZBinaryEqual) tests/AlignmentFile_test.py:490: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:447: in checkEcho self.assertTrue(checkf( E AssertionError: False is not true : files ex2.bam and tmp_ex2.bam are not the same _____________________ TestIO.testWriteUncompressedBAMFile ______________________ self = def testWriteUncompressedBAMFile(self): '''read from uncompressed BAM file, see issue #43''' input_filename = "ex2.sam" output_filename = "pysam_uncompressed.bam" reference_filename = "uncompressed.bam" > self.checkEcho(input_filename, reference_filename, output_filename, "r", "wb0") tests/AlignmentFile_test.py:780: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:447: in checkEcho self.assertTrue(checkf( E AssertionError: False is not true : files uncompressed.bam and pysam_uncompressed.bam are not the same ___________________ TestDeNovoConstruction.testBAMWholeFile ____________________ self = def testBAMWholeFile(self): tmpfilename = "tmp_%i.bam" % id(self) outfile = pysam.AlignmentFile(tmpfilename, "wb", header=self.header) for x in self.reads: outfile.write(x) outfile.close() > self.assertTrue( checkGZBinaryEqual(tmpfilename, self.bamfile), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) E AssertionError: False is not true : mismatch when construction BAM file, see tmp_139880666932512.bam /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex6.bam tests/AlignmentFile_test.py:1377: AssertionError _______________________ TestEmptyHeader.testEmptyHeader ________________________ self = def testEmptyHeader(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'example_empty_header.bam')) > self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]}) E AssertionError: OrderedDict([('SQ', [{'SN': 'chr1', 'LN':[119 chars]}])]) != {'SQ': [{'LN': 1000, 'SN': 'chr1'}]} tests/AlignmentFile_test.py:1406: AssertionError ___________________ TestHeaderWithProgramOptions.testHeader ____________________ self = def testHeader(self): > s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'rg_with_tab.bam')) tests/AlignmentFile_test.py:1447: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E FileNotFoundError: [Errno 2] could not open alignment file `/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory pysam/libcalignmentfile.pyx:940: FileNotFoundError _______________________ StreamTest.test_text_processing ________________________ self = @unittest.skipIf(IS_PYTHON2, "no context manager in py2") def test_text_processing(self): with subprocess.Popen('head -n200', stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) as proc: in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam')) out_stream = AlignmentFile( proc.stdin, 'wh', header=in_stream.header) writer = alignmentfile_writer_thread(in_stream, out_stream) written, read = self.stream_process(proc, in_stream, out_stream, writer) > self.assertEqual(read, 198) E AssertionError: 197 != 198 tests/StreamFiledescriptors_test.py:61: AssertionError =============================== warnings summary =============================== /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) .pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py:1471: UserWarning: no BGZF EOF marker; file may be truncated s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'), .pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py::SamtoolsTest::testStatements .pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py::PysamTest::testStatements /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py:136: UserWarning: versions of pysam.samtools and samtools differ: 1.9 != 1.10 warnings.warn( -- Docs: https://docs.pytest.org/en/latest/warnings.html ======= 20 failed, 907 passed, 10 skipped, 4 warnings in 108.20 seconds ======== make[1]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds' create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) Fixing /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8 creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tmp_139880666932512.bam -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/htslib_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/version.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/version.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam creating /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/__init__.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/samtools.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/Pileup.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/utils.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/config.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/bcftools.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/version.cpython-38.pyc -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-x86_64-linux-gnu.so -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/tmp_ex2.bam -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/pysam_uncompressed.bam -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages copying /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/.pybuild/cpython3_3.8_pysam/build/log.txt -> /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/samtools.py to samtools.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__init__.py to __init__.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/bcftools.py to bcftools.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/Pileup.py to Pileup.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/__init__.py to __init__.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/utils.py to utils.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/version.py to version.cpython-38.pyc byte-compiling /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/config.py to config.cpython-38.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/os/*.c' warning: no files found matching 'htslib/os/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam-0.15.4.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/pysam_data' rm -fr *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[2]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete make[1]: Leaving directory '/build/python-pysam-p3cTC6/python-pysam-0.15.4+ds' dh_installdocs -i -O--buildsystem=pybuild dh_installchangelogs -i -O--buildsystem=pybuild dh_python3 -i -O--buildsystem=pybuild E: dh_python3 dh_python3:176: no package to act on (python3-foo or one with ${python3:Depends} in Depends) dh_installinit -i -O--buildsystem=pybuild dh_installsystemduser -i -O--buildsystem=pybuild dh_lintian -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild dh_compress -i -O--buildsystem=pybuild dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.15.4+ds-3_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../python-pysam_0.15.4+ds-3_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/python-pysam-p3cTC6 /tmp/python-pysam-0.15.4+ds-3wb95kbw1 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.JMyu3HSbIG... I: success in 928.0169 seconds md5: python-pysam-tests_0.15.4+ds-3_all.deb: OK sha1: python-pysam-tests_0.15.4+ds-3_all.deb: OK sha256: python-pysam-tests_0.15.4+ds-3_all.deb: OK Checksums: OK