RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-002 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:20 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_142 python-lpbuildd_142 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.11. Syncing the system clock with the buildd NTP service... 14 May 14:34:40 ntpdate[1818]: adjust time server 10.211.37.1 offset 0.001027 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12582255', '/home/buildd/filecache-default/393420d2b09d3fd212076c1e7bb21902ac116e2c'] Unpacking chroot for build PACKAGEBUILD-12582255 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12582255'] Mounting chroot for build PACKAGEBUILD-12582255 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12582255', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-12582255 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12582255', 'arm64'] Updating debian chroot for build PACKAGEBUILD-12582255 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main arm64 Packages [1126 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [564 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe arm64 Packages [8013 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4749 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 Packages [52.1 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [25.1 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe arm64 Packages [116 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [69.6 kB] Fetched 15.3 MB in 6s (2321 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https binutils cpp-6 debianutils dmsetup dpkg dpkg-dev g++-6 gcc-6 gcc-6-base init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libcc1-0 libdevmapper1.02.1 libdpkg-perl libgcc-6-dev libgcc1 libgnutls30 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkmod2 libkrb5-26-heimdal libroken18-heimdal libselinux1 libstdc++-6-dev libstdc++6 libsystemd0 libubsan0 libudev1 libusb-0.1-4 libwind0-heimdal linux-libc-dev systemd systemd-sysv 48 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 31.1 MB of archives. After this operation, 674 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main arm64 debianutils arm64 4.8.1.1 [84.8 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main arm64 dpkg arm64 1.18.23ubuntu6 [1088 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 init-system-helpers all 1.48 [37.8 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main arm64 gcc-7-base arm64 7.1.0-4ubuntu1 [18.4 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main arm64 libgcc1 arm64 1:7.1.0-4ubuntu1 [33.6 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main arm64 libstdc++6 arm64 7.1.0-4ubuntu1 [385 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main arm64 libapt-pkg5.0 arm64 1.4.3 [720 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main arm64 apt arm64 1.4.3 [1068 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 libapparmor1 arm64 2.11.0-2ubuntu7 [26.7 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main arm64 libaudit-common all 1:2.6.6-1ubuntu2 [4626 B] Get:11 http://ftpmaster.internal/ubuntu artful/main arm64 libaudit1 arm64 1:2.6.6-1ubuntu2 [35.0 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main arm64 libkmod2 arm64 24-1ubuntu1 [31.7 kB] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 libselinux1 arm64 2.6-3build1 [55.5 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main arm64 systemd arm64 233-6ubuntu1 [2111 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main arm64 libsystemd0 arm64 233-6ubuntu1 [171 kB] Get:16 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 init arm64 1.48 [5806 B] Get:17 http://ftpmaster.internal/ubuntu artful/main arm64 systemd-sysv arm64 233-6ubuntu1 [13.6 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main arm64 libudev1 arm64 233-6ubuntu1 [48.2 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main arm64 libdevmapper1.02.1 arm64 2:1.02.137-2ubuntu1 [109 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main arm64 dmsetup arm64 2:1.02.137-2ubuntu1 [64.8 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main arm64 libroken18-heimdal arm64 7.1.0+dfsg-13 [34.3 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main arm64 libasn1-8-heimdal arm64 7.1.0+dfsg-13 [127 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main arm64 libgnutls30 arm64 3.5.8-5ubuntu1 [561 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main arm64 libheimbase1-heimdal arm64 7.1.0+dfsg-13 [24.1 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main arm64 libhcrypto4-heimdal arm64 7.1.0+dfsg-13 [74.2 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main arm64 libwind0-heimdal arm64 7.1.0+dfsg-13 [46.9 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main arm64 libhx509-5-heimdal arm64 7.1.0+dfsg-13 [86.8 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main arm64 libkrb5-26-heimdal arm64 7.1.0+dfsg-13 [166 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main arm64 libheimntlm0-heimdal arm64 7.1.0+dfsg-13 [13.3 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main arm64 libgssapi3-heimdal arm64 7.1.0+dfsg-13 [77.3 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main arm64 apt-transport-https arm64 1.4.3 [31.0 kB] Get:32 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 advancecomp arm64 1.23-1 [169 kB] Get:33 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 binutils arm64 2.28-5ubuntu1 [2552 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main arm64 libgomp1 arm64 7.1.0-4ubuntu1 [62.4 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main arm64 libitm1 arm64 7.1.0-4ubuntu1 [25.6 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main arm64 libubsan0 arm64 7.1.0-4ubuntu1 [112 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main arm64 libatomic1 arm64 7.1.0-4ubuntu1 [6624 B] Get:38 http://ftpmaster.internal/ubuntu artful/main arm64 libasan3 arm64 6.3.0-17ubuntu1 [275 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main arm64 g++-6 arm64 6.3.0-17ubuntu1 [5880 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main arm64 libstdc++-6-dev arm64 6.3.0-17ubuntu1 [1391 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main arm64 gcc-6 arm64 6.3.0-17ubuntu1 [5782 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main arm64 libgcc-6-dev arm64 6.3.0-17ubuntu1 [566 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main arm64 libcc1-0 arm64 7.1.0-4ubuntu1 [35.4 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main arm64 cpp-6 arm64 6.3.0-17ubuntu1 [5145 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main arm64 gcc-6-base arm64 6.3.0-17ubuntu1 [17.1 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main arm64 dpkg-dev all 1.18.23ubuntu6 [607 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main arm64 libdpkg-perl all 1.18.23ubuntu6 [209 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main arm64 libusb-0.1-4 arm64 2:0.1.12-31 [15.0 kB] Get:49 http://ftpmaster.internal/ubuntu artful-proposed/main arm64 linux-libc-dev arm64 4.10.0-21.23 [885 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.1 MB in 1s (29.8 MB/s) (Reading database ... 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Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12582255', 'arm64', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=arm64', '--dist=artful-proposed', '--purge=never', '--nolog', 'python-pysam_0.10.0+ds-2build1.dsc'] Initiating build PACKAGEBUILD-12582255 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:20 UTC 2017 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-002.buildd +==============================================================================+ | python-pysam 0.10.0+ds-2build1 (arm64) 14 May 2017 14:35 | +==============================================================================+ Package: python-pysam Version: 0.10.0+ds-2build1 Source Version: 0.10.0+ds-2build1 Distribution: artful-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/python-pysam-i4tife/python-pysam-0.10.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-i4tife' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12582255/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.10.0+ds-2build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-B2uWcd/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-B2uWcd/apt_archive ./ InRelease Get:2 copy:/<>/resolver-B2uWcd/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-B2uWcd/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-B2uWcd/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-B2uWcd/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (156 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-B2uWcd/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 12381 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose Filtered Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-yzowbb/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-yzowbb/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yzowbb/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yzowbb/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yzowbb/apt_archive ./ Sources [299 B] Get:5 copy:/<>/resolver-yzowbb/apt_archive ./ Packages [619 B] Fetched 3037 B in 0s (162 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-pysam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts1 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-dev python3.6-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python-coverage python-nose-doc python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.5-venv python3.5-doc python3.6-venv python3.6-doc Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgsl2 libhts-dev libhts1 libicu57 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-nose python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-nose python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal python3.6 python3.6-dev python3.6-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 87 newly installed, 1 to remove and 0 not upgraded. Need to get 70.8 MB of archives. After this operation, 238 MB of additional disk space will be used. 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Get:82 http://ftpmaster.internal/ubuntu artful/main arm64 python3-pkg-resources all 33.1.1-1 [97.9 kB] Get:83 http://ftpmaster.internal/ubuntu artful/universe arm64 python3-nose all 1.3.7-2 [116 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main arm64 python3-setuptools all 33.1.1-1 [175 kB] Get:85 http://ftpmaster.internal/ubuntu artful/universe arm64 samtools arm64 1.3.1-3 [227 kB] Get:86 http://ftpmaster.internal/ubuntu artful/universe arm64 tabix arm64 1.3.2-2ubuntu1 [206 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-0ubuntu1 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.8 MB in 4s (15.1 MB/s) (Reading database ... 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Setting up libpipeline1:arm64 (1.4.1-2) ... Setting up libgsl2:arm64 (2.3+dfsg-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:arm64 (57.1-6) ... Setting up libbsd0:arm64 (0.8.3-1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-2.2build1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:arm64 (1:5.30-1) ... Setting up libcroco3:arm64 (0.6.11-3) ... Setting up libpython3.6-minimal:arm64 (3.6.1-1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up libexpat1-dev:arm64 (2.2.0-2) ... Setting up tabix (1.3.2-2ubuntu1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up samtools (1.3.1-3) ... Setting up bcftools (1.3.1-1) ... Setting up libpython2.7-stdlib:arm64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libmpdec2:arm64 (2.4.2-1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.033-2) ... Setting up libpython3.6-stdlib:arm64 (3.6.1-1) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libpython3.5-stdlib:arm64 (3.5.3-1) ... Setting up python3.6-minimal (3.6.1-1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:arm64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython2.7:arm64 (2.7.13-2) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2.7-dev:arm64 (2.7.13-2) ... Setting up python2.7-dev (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libpython3.6:arm64 (3.6.1-1) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-1) ... Setting up libpython3-stdlib:arm64 (3.5.3-1ubuntu3) ... Setting up libpython-dev:arm64 (2.7.13-2) ... Setting up python3.6 (3.6.1-1) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:arm64 (3.5.3-1) ... Setting up python-dev (2.7.13-2) ... Setting up libpython-all-dev:arm64 (2.7.13-2) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up libpython3.6-dev:arm64 (3.6.1-1) ... Setting up libpython3.5-dev:arm64 (3.5.3-1) ... Setting up cython (0.25.2-1build1) ... Setting up python3.6-dev (3.6.1-1) ... Setting up python3.5-dev (3.5.3-1) ... Setting up python-nose (1.3.7-2) ... Setting up python-all (2.7.13-2) ... Setting up libpython3-dev:arm64 (3.5.3-1ubuntu3) ... Setting up python-setuptools (33.1.1-1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libpython3-all-dev:arm64 (3.5.3-1ubuntu3) ... Setting up dh-autoreconf (14) ... Setting up python3 (3.5.3-1ubuntu3) ... Setting up python3-dev (3.5.3-1ubuntu3) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up dh-strip-nondeterminism (0.033-2) ... Setting up python3-nose (1.3.7-2) ... Setting up python3-all (3.5.3-1ubuntu3) ... Setting up cython3 (0.25.2-1build1) ... Setting up python3-setuptools (33.1.1-1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.2.5ubuntu2) ... Setting up python3-all-dev (3.5.3-1ubuntu3) ... Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ... (Reading database ... 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Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-77-generic arm64 (aarch64) Toolchain package versions: binutils_2.28-5ubuntu1 dpkg-dev_1.18.23ubuntu6 g++-6_6.3.0-17ubuntu1 gcc-6_6.3.0-17ubuntu1 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-17ubuntu1 libstdc++6_7.1.0-4ubuntu1 linux-libc-dev_4.10.0-21.23 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.23-1 apt_1.4.3 apt-transport-https_1.4.3 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu99 base-passwd_3.5.43 bash_4.4-2ubuntu1 bcftools_1.3.1-1 binutils_2.28-5ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-17ubuntu1 cython_0.25.2-1build1 cython3_0.25.2-1build1 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.2.5ubuntu2 debianutils_4.8.1.1 dh-autoreconf_14 dh-python_2.20170125 dh-strip-nondeterminism_0.033-2 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu1 dpkg_1.18.23ubuntu6 dpkg-dev_1.18.23ubuntu6 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-2ubuntu1 g++-6_6.3.0-17ubuntu1 gcc_4:6.3.0-2ubuntu1 gcc-6_6.3.0-17ubuntu1 gcc-6-base_6.3.0-17ubuntu1 gcc-7-base_7.1.0-4ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu7 libapt-pkg5.0_1.4.3 libarchive-zip-perl_1.59-1 libasan3_6.3.0-17ubuntu1 libasn1-8-heimdal_7.1.0+dfsg-13 libassuan0_2.4.3-2 libatomic1_7.1.0-4ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.6.6-1ubuntu2 libaudit1_1:2.6.6-1ubuntu2 libblkid1_2.29-1ubuntu2 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-4ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu1 libdpkg-perl_1.18.23ubuntu6 libexpat1_2.2.0-2 libexpat1-dev_2.2.0-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu2 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.033-2 libgcc-6-dev_6.3.0-17ubuntu1 libgcc1_1:7.1.0-4ubuntu1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libglib2.0-0_2.53.1-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-5ubuntu1 libgomp1_7.1.0-4ubuntu1 libgpg-error0_1.26-2 libgsl2_2.3+dfsg-1 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-13 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhts-dev_1.3.2-2ubuntu1 libhts1_1.3.2-2ubuntu1 libhx509-5-heimdal_7.1.0+dfsg-13 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.18-1 libitm1_7.1.0-4ubuntu1 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-4ubuntu1 libldap-common_2.4.44+dfsg-4ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu2 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.3-1 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-3 libperl5.24_5.24.1-2ubuntu1 libpipeline1_1.4.1-2 libpng16-16_1.6.29-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-all-dev_3.5.3-1ubuntu3 libpython3-dev_3.5.3-1ubuntu3 libpython3-stdlib_3.5.3-1ubuntu3 libpython3.5_3.5.3-1 libpython3.5-dev_3.5.3-1 libpython3.5-minimal_3.5.3-1 libpython3.5-stdlib_3.5.3-1 libpython3.6_3.6.1-1 libpython3.6-dev_3.6.1-1 libpython3.6-minimal_3.6.1-1 libpython3.6-stdlib_3.6.1-1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-13 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu2 libsqlite3-0_3.16.2-3 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu12 libstdc++-6-dev_6.3.0-17ubuntu1 libstdc++6_7.1.0-4ubuntu1 libsystemd0_233-6ubuntu1 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.1.0-4ubuntu1 libudev1_233-6ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu2 libwind0-heimdal_7.1.0+dfsg-13 libxml2_2.9.4+dfsg1-2.2build1 linux-libc-dev_4.10.0-21.23 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu2 multiarch-support_2.24-9ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu12 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1build1 perl_5.24.1-2ubuntu1 perl-base_5.24.1-2ubuntu1 perl-modules-5.24_5.24.1-2ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-nose_1.3.7-2 python-pkg-resources_33.1.1-1 python-setuptools_33.1.1-1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1ubuntu3 python3-all_3.5.3-1ubuntu3 python3-all-dev_3.5.3-1ubuntu3 python3-dev_3.5.3-1ubuntu3 python3-minimal_3.5.3-1ubuntu3 python3-nose_1.3.7-2 python3-pkg-resources_33.1.1-1 python3-setuptools_33.1.1-1 python3.5_3.5.3-1 python3.5-dev_3.5.3-1 python3.5-minimal_3.5.3-1 python3.6_3.6.1-1 python3.6-dev_3.6.1-1 python3.6-minimal_3.6.1-1 readline-common_7.0-0ubuntu2 samtools_1.3.1-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-6ubuntu1 systemd-sysv_233-6ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.3.2-2ubuntu1 tar_1.29b-1.1 tzdata_2017b-1 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun May 14 14:33:10 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.10.0+ds-2build1.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.10.0+ds dpkg-source: info: unpacking python-pysam_0.10.0+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.10.0+ds-2build1.debian.tar.xz dpkg-source: info: applying rpath.patch dpkg-source: info: applying htslib-external-config.patch dpkg-source: info: applying exclude_test_tyring_to_access_remote_ftpserver.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/python-pysam-0.10.0+ds SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/python-pysam-0.10.0+ds' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.10.0+ds-2build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build python-pysam-0.10.0+ds dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.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 dh clean --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' dh_auto_clean I: pybuild base:184: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.6 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it I: pybuild base:184: python3.5 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.5' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_testdir -a -O--buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.6 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:184: python3.5 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 -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python 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 /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/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) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c building 'pysam.libchtslib' extension creating build creating build/temp.linux-arm64-2.7 creating build/temp.linux-arm64-2.7/pysam aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-arm64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-arm64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libchtslib.o build/temp.linux-arm64-2.7/pysam/htslib_util.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension creating build/temp.linux-arm64-2.7/samtools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-arm64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-arm64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-arm64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-arm64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcsamfile.o build/temp.linux-arm64-2.7/pysam/htslib_util.o build/temp.linux-arm64-2.7/pysam/samfile_util.o build/temp.linux-arm64-2.7/samtools/kprobaln.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-2.7/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:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-arm64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-arm64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-arm64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcalignmentfile.o build/temp.linux-arm64-2.7/pysam/htslib_util.o build/temp.linux-arm64-2.7/pysam/samfile_util.o build/temp.linux-arm64-2.7/samtools/kprobaln.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-arm64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-arm64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-arm64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o build/temp.linux-arm64-2.7/pysam/htslib_util.o build/temp.linux-arm64-2.7/pysam/samfile_util.o build/temp.linux-arm64-2.7/samtools/kprobaln.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so cythoning pysam/libctabix.pyx to pysam/libctabix.c building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-arm64-2.7/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:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-arm64-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libctabix.o build/temp.linux-arm64-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-arm64-2.7/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.66’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcvcf.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so cythoning pysam/libcbcf.pyx to pysam/libcbcf.c building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-arm64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbcf.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-arm64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbgzf.o -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-arm64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension creating build/temp.linux-arm64-2.7/bcftools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-arm64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:10530:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-arm64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp] #warning "No curses library is available; tview with curses is disabled." ^~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-2.7/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 ‘info_rules_init’: bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; ^~~~~ bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; ^~ bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; n++; ^~~~~ bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; n++; ^~ bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’: bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~ bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-CzRYjo/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcutils.o build/temp.linux-arm64-2.7/pysam/pysam_util.o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-2.7/samtools/faidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o build/temp.linux-arm64-2.7/samtools/padding.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-2.7/samtools/phase.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-2.7/samtools/errmod.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-arm64-2.7/samtools/sample.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-2.7/bcftools/convert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-2.7/bcftools/version.c.pysam.o build/temp.linux-arm64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mcall.c.pysam.o -Lpysam -L/usr/lib/aarch64-linux-gnu -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so I: pybuild base:184: /usr/bin/python3.6 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 /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/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) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/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 skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-arm64-3.6 creating build/temp.linux-arm64-3.6/pysam aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-arm64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libchtslib.o build/temp.linux-arm64-3.6/pysam/htslib_util.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension creating build/temp.linux-arm64-3.6/samtools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamfile.c -o build/temp.linux-arm64-3.6/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-arm64-3.6/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c samtools/kprobaln.c -o build/temp.linux-arm64-3.6/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcsamfile.o build/temp.linux-arm64-3.6/pysam/htslib_util.o build/temp.linux-arm64-3.6/pysam/samfile_util.o build/temp.linux-arm64-3.6/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-3.6/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:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-arm64-3.6/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c samtools/kprobaln.c -o build/temp.linux-arm64-3.6/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcalignmentfile.o build/temp.linux-arm64-3.6/pysam/htslib_util.o build/temp.linux-arm64-3.6/pysam/samfile_util.o build/temp.linux-arm64-3.6/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-3.6/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-arm64-3.6/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c samtools/kprobaln.c -o build/temp.linux-arm64-3.6/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcalignedsegment.o build/temp.linux-arm64-3.6/pysam/htslib_util.o build/temp.linux-arm64-3.6/pysam/samfile_util.o build/temp.linux-arm64-3.6/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libctabix.c -o build/temp.linux-arm64-3.6/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:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/tabix_util.c -o build/temp.linux-arm64-3.6/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libctabix.o build/temp.linux-arm64-3.6/pysam/tabix_util.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c pysam/libctabixproxies.c -o build/temp.linux-arm64-3.6/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libctabixproxies.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcvcf.c -o build/temp.linux-arm64-3.6/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.67’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcvcf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcf.c -o build/temp.linux-arm64-3.6/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcbcf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbgzf.c -o build/temp.linux-arm64-3.6/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcbgzf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbgzf.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcfaidx.c -o build/temp.linux-arm64-3.6/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcfaidx.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.cpython-36m-aarch64-linux-gnu.so skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension creating build/temp.linux-arm64-3.6/bcftools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcutils.c -o build/temp.linux-arm64-3.6/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:289:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/pysam_util.c -o build/temp.linux-arm64-3.6/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp] #warning "No curses library is available; tview with curses is disabled." ^~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/errmod.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-3.6/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-3.6/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 ‘info_rules_init’: bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; ^~~~~ bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; ^~ bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; n++; ^~~~~ bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; n++; ^~ bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’: bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~ bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-3.6/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/pysam/libcutils.o build/temp.linux-arm64-3.6/pysam/pysam_util.o build/temp.linux-arm64-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-3.6/samtools/faidx.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_tview_curses.c.pysam.o build/temp.linux-arm64-3.6/samtools/stats.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_split.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-3.6/samtools/cut_target.c.pysam.o build/temp.linux-arm64-3.6/samtools/dict.c.pysam.o build/temp.linux-arm64-3.6/samtools/padding.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-3.6/samtools/sam_view.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-3.6/samtools/phase.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_index.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-3.6/samtools/kprobaln.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam.c.pysam.o build/temp.linux-arm64-3.6/samtools/sam_header.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_md.c.pysam.o build/temp.linux-arm64-3.6/samtools/bedcov.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-3.6/samtools/errmod.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_import.c.pysam.o build/temp.linux-arm64-3.6/samtools/bamtk.c.pysam.o build/temp.linux-arm64-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-3.6/samtools/bedidx.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_tview_html.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_tview.c.pysam.o build/temp.linux-arm64-3.6/samtools/sample.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-3.6/samtools/bam_color.c.pysam.o build/temp.linux-arm64-3.6/samtools/sam.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-3.6/bcftools/HMM.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-3.6/bcftools/kmin.c.pysam.o build/temp.linux-arm64-3.6/bcftools/em.c.pysam.o build/temp.linux-arm64-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-3.6/bcftools/consensus.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-3.6/bcftools/convert.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-3.6/bcftools/ccall.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-3.6/bcftools/version.c.pysam.o build/temp.linux-arm64-3.6/bcftools/prob1.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-3.6/bcftools/filter.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-3.6/bcftools/main.c.pysam.o build/temp.linux-arm64-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-3.6/bcftools/tabix.c.pysam.o build/temp.linux-arm64-3.6/bcftools/mcall.c.pysam.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.cpython-36m-aarch64-linux-gnu.so I: pybuild base:184: /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 /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/version.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/config.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/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) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools creating /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/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 skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-arm64-3.5 creating build/temp.linux-arm64-3.5/pysam aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libchtslib.c -o build/temp.linux-arm64-3.5/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libchtslib.o build/temp.linux-arm64-3.5/pysam/htslib_util.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension creating build/temp.linux-arm64-3.5/samtools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcsamfile.c -o build/temp.linux-arm64-3.5/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-arm64-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-arm64-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcsamfile.o build/temp.linux-arm64-3.5/pysam/htslib_util.o build/temp.linux-arm64-3.5/pysam/samfile_util.o build/temp.linux-arm64-3.5/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-3.5/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:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); ^ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-arm64-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-arm64-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcalignmentfile.o build/temp.linux-arm64-3.5/pysam/htslib_util.o build/temp.linux-arm64-3.5/pysam/samfile_util.o build/temp.linux-arm64-3.5/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-3.5/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-arm64-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-arm64-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcalignedsegment.o build/temp.linux-arm64-3.5/pysam/htslib_util.o build/temp.linux-arm64-3.5/pysam/samfile_util.o build/temp.linux-arm64-3.5/samtools/kprobaln.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libctabix.c -o build/temp.linux-arm64-3.5/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:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-arm64-3.5/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libctabix.o build/temp.linux-arm64-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c pysam/libctabixproxies.c -o build/temp.linux-arm64-3.5/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libctabixproxies.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcvcf.c -o build/temp.linux-arm64-3.5/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.67’: pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcvcf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbcf.c -o build/temp.linux-arm64-3.5/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcbcf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbgzf.c -o build/temp.linux-arm64-3.5/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcbgzf.o -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbgzf.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcfaidx.c -o build/temp.linux-arm64-3.5/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcfaidx.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.cpython-35m-aarch64-linux-gnu.so skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension creating build/temp.linux-arm64-3.5/bcftools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcutils.c -o build/temp.linux-arm64-3.5/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:289:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-arm64-3.5/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp] #warning "No curses library is available; tview with curses is disabled." ^~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam.c.pysam.c: In function ‘bam_view1’: samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0; ^ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-3.5/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-3.5/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 ‘info_rules_init’: bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; ^~~~~ bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; ^~ bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] while ( *ss ) ss++; ss++; n++; ^~~~~ bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’ while ( *ss ) ss++; ss++; n++; ^~ bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’: bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~ bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (j=0; jnals; j++) fprintf(pysam_stderr,"%s %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n"); ^~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-3.5/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.10.0+ds=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.5/pysam/libcutils.o build/temp.linux-arm64-3.5/pysam/pysam_util.o build/temp.linux-arm64-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-3.5/samtools/faidx.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-3.5/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-arm64-3.5/samtools/stats.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_split.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-3.5/samtools/cut_target.c.pysam.o build/temp.linux-arm64-3.5/samtools/dict.c.pysam.o build/temp.linux-arm64-3.5/samtools/padding.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-3.5/samtools/sam_view.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-3.5/samtools/phase.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_index.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam.c.pysam.o build/temp.linux-arm64-3.5/samtools/sam_header.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_md.c.pysam.o build/temp.linux-arm64-3.5/samtools/bedcov.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-3.5/samtools/errmod.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_import.c.pysam.o build/temp.linux-arm64-3.5/samtools/bamtk.c.pysam.o build/temp.linux-arm64-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-3.5/samtools/bedidx.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-arm64-3.5/samtools/sample.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-3.5/samtools/bam_color.c.pysam.o build/temp.linux-arm64-3.5/samtools/sam.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-3.5/bcftools/HMM.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-3.5/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-3.5/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-3.5/bcftools/kmin.c.pysam.o build/temp.linux-arm64-3.5/bcftools/em.c.pysam.o build/temp.linux-arm64-3.5/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-3.5/bcftools/consensus.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-3.5/bcftools/convert.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-3.5/bcftools/ccall.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-3.5/bcftools/version.c.pysam.o build/temp.linux-arm64-3.5/bcftools/prob1.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-3.5/bcftools/filter.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-3.5/bcftools/main.c.pysam.o build/temp.linux-arm64-3.5/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-3.5/bcftools/tabix.c.pysam.o build/temp.linux-arm64-3.5/bcftools/mcall.c.pysam.o -Lpysam -lz -lhts -o /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.cpython-35m-aarch64-linux-gnu.so debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 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 view -buS ex2.sam > uncompressed.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS example_empty_with_header.sam > example_empty_with_header.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 test_unaligned.sam > test_unaligned.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 ex6.sam > ex6.bam samtools view -bS rg_with_tab.sam > rg_with_tab.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 import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam rm -f tmp.list samtools view -bS ex4.sam > ex4.bam samtools view -bS example_user_header.sam > example_user_header.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index example_empty_with_header.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 test_unaligned.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index ex5.bam samtools index ex6.bam samtools index rg_with_tab.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 example_user_header.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 make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.10.0+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 < 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_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 missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.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 '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' dh_auto_test I: pybuild base:184: cd /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose reference bases should always be the same nucleotide ... ok testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok check comparison functions. ... ok testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok see issue 26 ... ok testHashing (AlignedSegment_test.TestAlignedSegment) ... ok build an example read. ... ok issue 176: retrieving length without query sequence ... ok testPositions (AlignedSegment_test.TestAlignedSegment) ... ok see issue 62 ... ok testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok testAsString (AlignedSegment_test.TestAsString) ... ok testStats (AlignedSegment_test.TestCigarStats) ... ok testCopy (AlignedSegment_test.TestCopy) ... ok testDeepCopy (AlignedSegment_test.TestCopy) ... ok testAddTags (AlignedSegment_test.TestTags) ... ok testAddTagsType (AlignedSegment_test.TestTags) ... ok testArrayTags (AlignedSegment_test.TestTags) ... ok testEmptyTag (AlignedSegment_test.TestTags) ... ok testMDTagComplex (AlignedSegment_test.TestTags) ... ok testMDTagDeletions (AlignedSegment_test.TestTags) ... ok testMDTagInsertions (AlignedSegment_test.TestTags) ... ok testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok testMissingTag (AlignedSegment_test.TestTags) ... ok testSetTag (AlignedSegment_test.TestTags) ... ok test for tag parsing ... ok testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testRaises (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testTags (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testIndex (AlignmentFile_test.TestAlignmentFileIndex) ... ok testCount (AlignmentFile_test.TestAlignmentFileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok test BAM autodetection. ... ok test CRAM autodetection. ... ok test SAM autodetection. ... ok testReadTags (AlignmentFile_test.TestBTagBam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagBam) ... ok testReadTags (AlignmentFile_test.TestBTagSam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagSam) ... ok testClipping (AlignmentFile_test.TestClipping) ... ok testManager (AlignmentFile_test.TestContextManager) ... ok test_count_coverage (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_nofilter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_quality_filter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_all (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_callback (AlignmentFile_test.TestCountCoverage) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testEmptyHeader (AlignmentFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (AlignmentFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (AlignmentFile_test.TestExceptions) ... ok testBadContig (AlignmentFile_test.TestExceptions) ... ok testMeaninglessCrap (AlignmentFile_test.TestExceptions) ... ok testMissingFile (AlignmentFile_test.TestExceptions) ... ok testOutOfRangNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (AlignmentFile_test.TestExceptions) ... ok see issue 44 ... ok testExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... Warning: The index file is older than the data file: /<>/python-pysam-0.10.0+ds/tests/pysam_data/ex1.bam.bai ok testExplicitIndexCRAM (AlignmentFile_test.TestExplicitIndex) ... ok testRemoteExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... ok test_all (AlignmentFile_test.TestFindIntrons) ... ok test_first (AlignmentFile_test.TestFindIntrons) ... ok test_total (AlignmentFile_test.TestFindIntrons) ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (AlignmentFile_test.TestHeader1000Genomes) ... ok testHeaders (AlignmentFile_test.TestHeaderBAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderBAM) ... ok testHeaders (AlignmentFile_test.TestHeaderCRAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderCRAM) ... ok testHeaders (AlignmentFile_test.TestHeaderSAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderSAM) ... ok testHeader (AlignmentFile_test.TestHeaderWithProgramOptions) ... ok test_BAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_CRAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_SAM (AlignmentFile_test.TestHeaderWriteRead) ... ok testBAM2BAM (AlignmentFile_test.TestIO) ... ok testBAM2CRAM (AlignmentFile_test.TestIO) ... ok testBAM2SAM (AlignmentFile_test.TestIO) ... ok see issue 116 ... ok see issue 116 ... ok see issue 117 ... ok testCRAM2BAM (AlignmentFile_test.TestIO) ... ok testCRAM2CRAM (AlignmentFile_test.TestIO) ... ok testCRAM2SAM (AlignmentFile_test.TestIO) ... ok test that access to a closed samfile raises ValueError. ... ok testEmptyBAM (AlignmentFile_test.TestIO) ... ok testEmptyWithHeaderBAM (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFile (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFileObject (AlignmentFile_test.TestIO) ... ok test IteratorRowHead ... ok testOpenFromFilename (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok testReadSamWithoutHeader (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok read from bam file without index. ... ok testSAM2BAM (AlignmentFile_test.TestIO) ... ok testSAM2CRAM (AlignmentFile_test.TestIO) ... ok testSAM2SAM (AlignmentFile_test.TestIO) ... ok testSAM2SAMWithoutHeader (AlignmentFile_test.TestIO) ... ok read from uncompressed BAM file, see issue #43 ... ok see issue 131 ... ok testStart (AlignmentFile_test.TestIteratorColumn2) ... ok test if PileupRead can be printed. ... ok see issue 107. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok when creating a read with a large entry in the tag field ... ok testBAM (AlignmentFile_test.TestLargeOptValues) ... ok testSAM (AlignmentFile_test.TestLargeOptValues) ... ok testFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail2 (AlignmentFile_test.TestLogging) ... ok testMapped (AlignmentFile_test.TestMappedUnmapped) ... ok testAllStepper (AlignmentFile_test.TestPileup) ... ok testSamtoolsStepper (AlignmentFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (AlignmentFile_test.TestPileupObjects) ... ok testPileupRead (AlignmentFile_test.TestPileupObjects) ... ok testPileup (AlignmentFile_test.TestPileupQueryPosition) ... ok testFTPFetch (AlignmentFile_test.TestRemoteFileFTP) ... ok testFTPView (AlignmentFile_test.TestRemoteFileFTP) ... ok testFetch (AlignmentFile_test.TestRemoteFileHTTP) ... ok testFetchAll (AlignmentFile_test.TestRemoteFileHTTP) ... ok testView (AlignmentFile_test.TestRemoteFileHTTP) ... ok testIndex (AlignmentFile_test.TestSamtoolsProxy) ... ok testSort (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok test_empty_read_gives_value_error (AlignmentFile_test.TestSanityCheckingBAM) ... ok testArrayTags (AlignmentFile_test.TestTagParsing) ... ok testCigar (AlignmentFile_test.TestTagParsing) ... ok testCigarString (AlignmentFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (AlignmentFile_test.TestTagParsing) ... ok testNegativeIntegers2 (AlignmentFile_test.TestTagParsing) ... ok testTruncatedBam (AlignmentFile_test.TestTruncatedBAM) ... [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. [E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes ok See comments for pull request at ... ok testBAM (AlignmentFile_test.TestUnmappedReads) ... ok testVerbosity (AlignmentFile_test.TestVerbosity) ... ok testOpenBamAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenSamAsBam (AlignmentFile_test.TestWrongFormat) ... ok testARcigar (SamFile_test.BasicTestBAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestBAMFetch) ... ok testARflag (SamFile_test.BasicTestBAMFetch) ... ok testARisize (SamFile_test.BasicTestBAMFetch) ... ok testARmapq (SamFile_test.BasicTestBAMFetch) ... ok testARmpos (SamFile_test.BasicTestBAMFetch) ... ok testARmrnm (SamFile_test.BasicTestBAMFetch) ... ok testARpos (SamFile_test.BasicTestBAMFetch) ... ok testARqname (SamFile_test.BasicTestBAMFetch) ... ok testARqqual (SamFile_test.BasicTestBAMFetch) ... ok testARqual (SamFile_test.BasicTestBAMFetch) ... ok testARquery (SamFile_test.BasicTestBAMFetch) ... ok testARrname (SamFile_test.BasicTestBAMFetch) ... ok testARseq (SamFile_test.BasicTestBAMFetch) ... ok testAddTags (SamFile_test.BasicTestBAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestBAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestBAMFetch) ... ok testOpt (SamFile_test.BasicTestBAMFetch) ... ok testPairedBools (SamFile_test.BasicTestBAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFetch) ... ok testTags (SamFile_test.BasicTestBAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFetch) ... ok testARcigar (SamFile_test.BasicTestBAMFile) ... ok testARcigarstring (SamFile_test.BasicTestBAMFile) ... ok testARflag (SamFile_test.BasicTestBAMFile) ... ok testARisize (SamFile_test.BasicTestBAMFile) ... ok testARmapq (SamFile_test.BasicTestBAMFile) ... ok testARmpos (SamFile_test.BasicTestBAMFile) ... ok testARmrnm (SamFile_test.BasicTestBAMFile) ... ok testARpos (SamFile_test.BasicTestBAMFile) ... ok testARqname (SamFile_test.BasicTestBAMFile) ... ok testARqqual (SamFile_test.BasicTestBAMFile) ... ok testARqual (SamFile_test.BasicTestBAMFile) ... ok testARquery (SamFile_test.BasicTestBAMFile) ... ok testARrname (SamFile_test.BasicTestBAMFile) ... ok testARseq (SamFile_test.BasicTestBAMFile) ... ok testAddTags (SamFile_test.BasicTestBAMFile) ... ok testAddTagsType (SamFile_test.BasicTestBAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFile) ... ok testMissingOpt (SamFile_test.BasicTestBAMFile) ... ok testOpt (SamFile_test.BasicTestBAMFile) ... ok testPairedBools (SamFile_test.BasicTestBAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFile) ... ok testTags (SamFile_test.BasicTestBAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFile) ... ok testARcigar (SamFile_test.BasicTestSAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestSAMFetch) ... ok testARflag (SamFile_test.BasicTestSAMFetch) ... ok testARisize (SamFile_test.BasicTestSAMFetch) ... ok testARmapq (SamFile_test.BasicTestSAMFetch) ... ok testARmpos (SamFile_test.BasicTestSAMFetch) ... ok testARmrnm (SamFile_test.BasicTestSAMFetch) ... ok testARpos (SamFile_test.BasicTestSAMFetch) ... ok testARqname (SamFile_test.BasicTestSAMFetch) ... ok testARqqual (SamFile_test.BasicTestSAMFetch) ... ok testARqual (SamFile_test.BasicTestSAMFetch) ... ok testARquery (SamFile_test.BasicTestSAMFetch) ... ok testARrname (SamFile_test.BasicTestSAMFetch) ... ok testARseq (SamFile_test.BasicTestSAMFetch) ... ok testAddTags (SamFile_test.BasicTestSAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestSAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestSAMFetch) ... ok testOpt (SamFile_test.BasicTestSAMFetch) ... ok testPairedBools (SamFile_test.BasicTestSAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFetch) ... ok testTags (SamFile_test.BasicTestSAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFetch) ... ok testARcigar (SamFile_test.BasicTestSAMFile) ... ok testARcigarstring (SamFile_test.BasicTestSAMFile) ... ok testARflag (SamFile_test.BasicTestSAMFile) ... ok testARisize (SamFile_test.BasicTestSAMFile) ... ok testARmapq (SamFile_test.BasicTestSAMFile) ... ok testARmpos (SamFile_test.BasicTestSAMFile) ... ok testARmrnm (SamFile_test.BasicTestSAMFile) ... ok testARpos (SamFile_test.BasicTestSAMFile) ... ok testARqname (SamFile_test.BasicTestSAMFile) ... ok testARqqual (SamFile_test.BasicTestSAMFile) ... ok testARqual (SamFile_test.BasicTestSAMFile) ... ok testARquery (SamFile_test.BasicTestSAMFile) ... ok testARrname (SamFile_test.BasicTestSAMFile) ... ok testARseq (SamFile_test.BasicTestSAMFile) ... ok testAddTags (SamFile_test.BasicTestSAMFile) ... ok testAddTagsType (SamFile_test.BasicTestSAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFile) ... ok testMissingOpt (SamFile_test.BasicTestSAMFile) ... ok testOpt (SamFile_test.BasicTestSAMFile) ... ok testPairedBools (SamFile_test.BasicTestSAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFile) ... ok testTags (SamFile_test.BasicTestSAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFile) ... ok testBlocks (SamFile_test.TestAlignedRead) ... ok testEmpty (SamFile_test.TestAlignedRead) ... ok build an example read. ... ok testPositions (SamFile_test.TestAlignedRead) ... ok testStrOfEmptyRead (SamFile_test.TestAlignedRead) ... ok test for tag parsing ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok testReadTags (SamFile_test.TestBTagBam) ... ok testReadWriteTags (SamFile_test.TestBTagBam) ... ok testReadTags (SamFile_test.TestBTagSam) ... ok testReadWriteTags (SamFile_test.TestBTagSam) ... ok testClipping (SamFile_test.TestClipping) ... ok testManager (SamFile_test.TestContextManager) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchUntilEOF (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchWithRegion (SamFile_test.TestDoubleFetch) ... ok testEmptyHeader (SamFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (SamFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (SamFile_test.TestExceptions) ... ok testBadContig (SamFile_test.TestExceptions) ... ok testMeaninglessCrap (SamFile_test.TestExceptions) ... ok testMissingFile (SamFile_test.TestExceptions) ... ok testOutOfRangNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (SamFile_test.TestExceptions) ... ok see issue 44 ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (SamFile_test.TestHeader1000Genomes) ... ok testHeaders (SamFile_test.TestHeaderBam) ... ok testNameMapping (SamFile_test.TestHeaderBam) ... ok testHeaders (SamFile_test.TestHeaderSam) ... ok testNameMapping (SamFile_test.TestHeaderSam) ... ok test if autodetection works. ... ok see issue 116 ... ok see issue 117 ... ok test that access to a closed samfile raises ValueError. ... ok testFetchFromClosedFile (SamFile_test.TestIO) ... ok test IteratorRowHead ... ok see issue 104. ... ok testReadSamWithoutHeader (SamFile_test.TestIO) ... ok see issue 104. ... ok testReadWriteBam (SamFile_test.TestIO) ... ok testReadWriteSamWithHeader (SamFile_test.TestIO) ... ok testReadWriteSamWithoutHeader (SamFile_test.TestIO) ... ok read from bam file without index. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok see issue 131 ... ok testStart (SamFile_test.TestIteratorColumn2) ... ok see issue 107. ... ok check random access per contig ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok when creating a read with a large entry in the tag field ... ok testBAM (SamFile_test.TestLargeOptValues) ... ok testSAM (SamFile_test.TestLargeOptValues) ... ok testFail1 (SamFile_test.TestLogging) ... ok testNoFail1 (SamFile_test.TestLogging) ... ok testNoFail2 (SamFile_test.TestLogging) ... ok testAllStepper (SamFile_test.TestPileup) ... ok testSamtoolsStepper (SamFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (SamFile_test.TestPileupObjects) ... ok testPileupRead (SamFile_test.TestPileupObjects) ... ok testFTPFetch (SamFile_test.TestRemoteFileFTP) ... ok testFTPView (SamFile_test.TestRemoteFileFTP) ... ok testFetch (SamFile_test.TestRemoteFileHTTP) ... ok testFetchAll (SamFile_test.TestRemoteFileHTTP) ... ok testView (SamFile_test.TestRemoteFileHTTP) ... ok testIndex (SamFile_test.TestSamfileIndex) ... ok testCount (SamFile_test.TestSamfileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok testIndex (SamFile_test.TestSamtoolsProxy) ... ok testSort (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testCigar (SamFile_test.TestTagParsing) ... ok testCigarString (SamFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (SamFile_test.TestTagParsing) ... ok testNegativeIntegers2 (SamFile_test.TestTagParsing) ... ok testBAM (SamFile_test.TestUnmappedReads) ... ok testOpenBamAsSam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (SamFile_test.TestWrongFormat) ... ok testOpenSamAsBam (SamFile_test.TestWrongFormat) ... ok test_samtools_processing (StreamFiledescriptors_test.StreamTest) ... ok test_text_processing (StreamFiledescriptors_test.StreamTest) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testBase (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFWithContigs) ... ok testIterator (VariantFile_test.TestHeader) ... ok testStr (VariantFile_test.TestHeader) ... ok testOpen (VariantFile_test.TestIndexFilename) ... ok testVCF (VariantFile_test.TestMissingGenotypes) ... ok testVCFGZ (VariantFile_test.TestMissingGenotypes) ... ok testDetectBCF (VariantFile_test.TestOpening) ... ok testDetectVCF (VariantFile_test.TestOpening) ... [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.) ok testDetectVCFGZ (VariantFile_test.TestOpening) ... ok testEmptyFileVCF (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZOnlyHeader (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithoutIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFOnlyHeader (VariantFile_test.TestOpening) ... ok testMissingFile (VariantFile_test.TestOpening) ... ok testMissingFileVCFGZ (VariantFile_test.TestOpening) ... ok testAlleles (VariantFile_test.TestParsing) ... ok testAlt (VariantFile_test.TestParsing) ... ok testChrom (VariantFile_test.TestParsing) ... ok testFilter (VariantFile_test.TestParsing) ... ok testFormat (VariantFile_test.TestParsing) ... ok testId (VariantFile_test.TestParsing) ... ok testInfo (VariantFile_test.TestParsing) ... ok testPos (VariantFile_test.TestParsing) ... ok testQual (VariantFile_test.TestParsing) ... ok testRef (VariantFile_test.TestParsing) ... ok testSampleAlleleIndices (VariantFile_test.TestParsing) ... ok testSampleAlleles (VariantFile_test.TestParsing) ... ok testSampleFormats (VariantFile_test.TestParsing) ... ok testStart (VariantFile_test.TestParsing) ... ok testStop (VariantFile_test.TestParsing) ... ok testBase (VariantFile_test.TestSettingRecordValues) ... ok testGenotype (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSetQual (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSubsetting (VariantFile_test.TestSubsetting) ... ok In file included from /<>/python-pysam-0.10.0+ds/tests/_compile_test.c:439:0: /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ testCount (compile_test.BAMTest) ... ok testCount (compile_test.GTFTest) ... ok testFetch (faidx_test.TestFastaFile) ... ok testFetchErrors (faidx_test.TestFastaFile) ... ok testLength (faidx_test.TestFastaFile) ... ok test out of range access. ... ok testSequenceLengths (faidx_test.TestFastaFile) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndex) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testCounts (faidx_test.TestFastqFileFastq) ... ok testManager (faidx_test.TestFastqFileFastq) ... ok testMissingFile (faidx_test.TestFastqFileFastq) ... ok testSequence (faidx_test.TestFastqFileFastq) ... ok testCounts (faidx_test.TestFastxFileFasta) ... ok testManager (faidx_test.TestFastxFileFasta) ... ok testMissingFile (faidx_test.TestFastxFileFasta) ... ok testSequence (faidx_test.TestFastxFileFasta) ... ok testCounts (faidx_test.TestFastxFileFastq) ... ok testManager (faidx_test.TestFastxFileFastq) ... ok testMissingFile (faidx_test.TestFastxFileFastq) ... ok testSequence (faidx_test.TestFastxFileFastq) ... ok testCounts (faidx_test.TestFastxFileFastqStream) ... ok testManager (faidx_test.TestFastxFileFastqStream) ... ok testMissingFile (faidx_test.TestFastxFileFastqStream) ... ok testSequence (faidx_test.TestFastxFileFastqStream) ... ok testIteration (faidx_test.TestFastxFileWithEmptySequence) ... ok testStatements (samtools_test.BcftoolsTest) ... [W::bcf_hdr_check_sanity] GL should be declared as Number=G ok testEmptyIndex (samtools_test.EmptyIndexTest) ... ok testStatements (samtools_test.PysamTest) ... ok testStatements (samtools_test.SamtoolsTest) ... ok testDoubleCalling (samtools_test.StdoutTest) ... ok testSaveStdout (samtools_test.StdoutTest) ... ok testWithRedirectedStdout (samtools_test.StdoutTest) ... ok testWithoutRedirectedStdout (samtools_test.StdoutTest) ... ok testReturnValueData (samtools_test.TestReturnType) ... ok testReturnValueString (samtools_test.TestReturnType) ... ok testBED (tabix_test.TestBackwardsCompatibility) ... ok testBED0v23 (tabix_test.TestBackwardsCompatibility) ... ok testBED0v26 (tabix_test.TestBackwardsCompatibility) ... ok testEmpty (tabix_test.TestBackwardsCompatibility) ... ok testVCF (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v23 (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v26 (tabix_test.TestBackwardsCompatibility) ... ok testRead (tabix_test.TestBed) ... ok testWrite (tabix_test.TestBed) ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok testManager (tabix_test.TestContextManager) ... ok testCopy (tabix_test.TestGTF) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestGTF) ... ok testSetting (tabix_test.TestGTF) ... ok testUnset (tabix_test.TestGTF) ... ok testWrite (tabix_test.TestGTF) ... ok testAll (tabix_test.TestGZFile) ... ok testFetchAll (tabix_test.TestIndexArgument) ... ok test indexing via preset. ... ok testGTFTooFewFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testGTFTooManyFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testAll (tabix_test.TestIterationWithComments) ... ok testGetContigs (tabix_test.TestIterationWithComments) ... ok testHeader (tabix_test.TestIterationWithComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithComments) ... ok testPerContig (tabix_test.TestIterationWithComments) ... ok testPerContig2 (tabix_test.TestIterationWithComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithComments) ... ok testPerInterval (tabix_test.TestIterationWithComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok testAll (tabix_test.TestIterationWithoutComments) ... ok testGetContigs (tabix_test.TestIterationWithoutComments) ... ok testHeader (tabix_test.TestIterationWithoutComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithoutComments) ... ok testPerContig (tabix_test.TestIterationWithoutComments) ... ok testPerContig2 (tabix_test.TestIterationWithoutComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithoutComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithoutComments) ... ok testPerInterval (tabix_test.TestIterationWithoutComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIterators) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileCompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileUncompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsGenericCompressed) ... ok testDisjointIterators (tabix_test.TestMultipleIterators) ... ok testDoubleFetch (tabix_test.TestMultipleIterators) ... ok testJoinedIterators (tabix_test.TestMultipleIterators) ... ok testScope (tabix_test.TestMultipleIterators) ... ok testCopy (tabix_test.TestParser) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestParser) ... ok testUnset (tabix_test.TestParser) ... ok testWrite (tabix_test.TestParser) ... ok testFetchAll (tabix_test.TestRemoteFileHTTP) ... ok testHeader (tabix_test.TestRemoteFileHTTP) ... ok testRead (tabix_test.TestVCFFromTabix) ... ok testWrite (tabix_test.TestVCFFromTabix) ... ok testConnecting (tabix_test.TestVCFFromVCF) ... ok testParsing (tabix_test.TestVCFFromVCF) ... ok testConnecting (tabix_test.TestVCFFromVariantFile) ... ok testParsing (tabix_test.TestVCFFromVariantFile) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_10) ... ok testParsing (tabix_test.TestVCFFromVariantFile_10) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_11) ... ok testParsing (tabix_test.TestVCFFromVariantFile_11) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_12) ... ok testParsing (tabix_test.TestVCFFromVariantFile_12) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_13) ... ok testParsing (tabix_test.TestVCFFromVariantFile_13) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_15) ... ok testParsing (tabix_test.TestVCFFromVariantFile_15) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_16) ... ok testParsing (tabix_test.TestVCFFromVariantFile_16) ... [W::bcf_hdr_check_sanity] PL should be declared as Number=G [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_18) ... ok testParsing (tabix_test.TestVCFFromVariantFile_18) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_2) ... ok testParsing (tabix_test.TestVCFFromVariantFile_2) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_20) ... ok testParsing (tabix_test.TestVCFFromVariantFile_20) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_21) ... ok testParsing (tabix_test.TestVCFFromVariantFile_21) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_22) ... ok testParsing (tabix_test.TestVCFFromVariantFile_22) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_23) ... ok testParsing (tabix_test.TestVCFFromVariantFile_23) ... [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_24) ... ok testParsing (tabix_test.TestVCFFromVariantFile_24) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_3) ... ok testParsing (tabix_test.TestVCFFromVariantFile_3) ... [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_4) ... ok testParsing (tabix_test.TestVCFFromVariantFile_4) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_5) ... ok testParsing (tabix_test.TestVCFFromVariantFile_5) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_6) ... ok testParsing (tabix_test.TestVCFFromVariantFile_6) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_7) ... ok testParsing (tabix_test.TestVCFFromVariantFile_7) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_8) ... ok testParsing (tabix_test.TestVCFFromVariantFile_8) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_9) ... ok testParsing (tabix_test.TestVCFFromVariantFile_9) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_issue85) ... ok testParsing (tabix_test.TestVCFFromVariantFile_issue85) ... ok testConnecting (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testParsing (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testRead (tabix_test.VCFFromTabixTest_10) ... ok testWrite (tabix_test.VCFFromTabixTest_10) ... ok testRead (tabix_test.VCFFromTabixTest_11) ... ok testWrite (tabix_test.VCFFromTabixTest_11) ... ok testRead (tabix_test.VCFFromTabixTest_12) ... ok testWrite (tabix_test.VCFFromTabixTest_12) ... ok testRead (tabix_test.VCFFromTabixTest_13) ... ok testWrite (tabix_test.VCFFromTabixTest_13) ... ok testRead (tabix_test.VCFFromTabixTest_15) ... ok testWrite (tabix_test.VCFFromTabixTest_15) ... ok testRead (tabix_test.VCFFromTabixTest_16) ... ok testWrite (tabix_test.VCFFromTabixTest_16) ... ok testRead (tabix_test.VCFFromTabixTest_18) ... ok testWrite (tabix_test.VCFFromTabixTest_18) ... ok testRead (tabix_test.VCFFromTabixTest_2) ... ok testWrite (tabix_test.VCFFromTabixTest_2) ... ok testRead (tabix_test.VCFFromTabixTest_20) ... ok testWrite (tabix_test.VCFFromTabixTest_20) ... ok testRead (tabix_test.VCFFromTabixTest_21) ... ok testWrite (tabix_test.VCFFromTabixTest_21) ... ok testRead (tabix_test.VCFFromTabixTest_22) ... ok testWrite (tabix_test.VCFFromTabixTest_22) ... ok testRead (tabix_test.VCFFromTabixTest_23) ... ok testWrite (tabix_test.VCFFromTabixTest_23) ... ok testRead (tabix_test.VCFFromTabixTest_24) ... ok testWrite (tabix_test.VCFFromTabixTest_24) ... ok testRead (tabix_test.VCFFromTabixTest_3) ... ok testWrite (tabix_test.VCFFromTabixTest_3) ... ok testRead (tabix_test.VCFFromTabixTest_4) ... ok testWrite (tabix_test.VCFFromTabixTest_4) ... ok testRead (tabix_test.VCFFromTabixTest_5) ... ok testWrite (tabix_test.VCFFromTabixTest_5) ... ok testRead (tabix_test.VCFFromTabixTest_6) ... ok testWrite (tabix_test.VCFFromTabixTest_6) ... ok testRead (tabix_test.VCFFromTabixTest_7) ... ok testWrite (tabix_test.VCFFromTabixTest_7) ... ok testRead (tabix_test.VCFFromTabixTest_8) ... ok testWrite (tabix_test.VCFFromTabixTest_8) ... ok testRead (tabix_test.VCFFromTabixTest_9) ... ok testWrite (tabix_test.VCFFromTabixTest_9) ... ok testRead (tabix_test.VCFFromTabixTest_issue85) ... ok testWrite (tabix_test.VCFFromTabixTest_issue85) ... ok testRead (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testWrite (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testConnecting (tabix_test.VCFFromVCFTest_10) ... ok testParsing (tabix_test.VCFFromVCFTest_10) ... ok testConnecting (tabix_test.VCFFromVCFTest_11) ... ok testParsing (tabix_test.VCFFromVCFTest_11) ... ok testConnecting (tabix_test.VCFFromVCFTest_12) ... ok testParsing (tabix_test.VCFFromVCFTest_12) ... ok testConnecting (tabix_test.VCFFromVCFTest_13) ... ok testParsing (tabix_test.VCFFromVCFTest_13) ... ok testConnecting (tabix_test.VCFFromVCFTest_15) ... ok testParsing (tabix_test.VCFFromVCFTest_15) ... ok testConnecting (tabix_test.VCFFromVCFTest_16) ... ok testParsing (tabix_test.VCFFromVCFTest_16) ... ok testConnecting (tabix_test.VCFFromVCFTest_18) ... ok testParsing (tabix_test.VCFFromVCFTest_18) ... ok testConnecting (tabix_test.VCFFromVCFTest_2) ... ok testParsing (tabix_test.VCFFromVCFTest_2) ... ok testConnecting (tabix_test.VCFFromVCFTest_20) ... ok testParsing (tabix_test.VCFFromVCFTest_20) ... ok testConnecting (tabix_test.VCFFromVCFTest_21) ... ok testParsing (tabix_test.VCFFromVCFTest_21) ... ok testConnecting (tabix_test.VCFFromVCFTest_22) ... ok testParsing (tabix_test.VCFFromVCFTest_22) ... ok testConnecting (tabix_test.VCFFromVCFTest_23) ... ok testParsing (tabix_test.VCFFromVCFTest_23) ... ok testConnecting (tabix_test.VCFFromVCFTest_24) ... ok testParsing (tabix_test.VCFFromVCFTest_24) ... ok testConnecting (tabix_test.VCFFromVCFTest_3) ... ok testParsing (tabix_test.VCFFromVCFTest_3) ... ok testConnecting (tabix_test.VCFFromVCFTest_4) ... ok testParsing (tabix_test.VCFFromVCFTest_4) ... ok testConnecting (tabix_test.VCFFromVCFTest_5) ... ok testParsing (tabix_test.VCFFromVCFTest_5) ... ok testConnecting (tabix_test.VCFFromVCFTest_6) ... ok testParsing (tabix_test.VCFFromVCFTest_6) ... ok testConnecting (tabix_test.VCFFromVCFTest_7) ... ok testParsing (tabix_test.VCFFromVCFTest_7) ... ok testConnecting (tabix_test.VCFFromVCFTest_8) ... ok testParsing (tabix_test.VCFFromVCFTest_8) ... ok testConnecting (tabix_test.VCFFromVCFTest_9) ... ok testParsing (tabix_test.VCFFromVCFTest_9) ... ok testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok test_samtools_python.test_idxstats_parse_split_lines ... ok test_samtools_python.test_bedcov_split_lines ... ok test_samtools_python.test_idxstats_parse ... ok test_samtools_python.test_bedcov ... ok ---------------------------------------------------------------------- Ran 915 tests in 236.642s OK (0, 0) I: pybuild base:184: cd /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose reference bases should always be the same nucleotide ... ok testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok check comparison functions. ... ok testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok see issue 26 ... ok testHashing (AlignedSegment_test.TestAlignedSegment) ... ok build an example read. ... ok issue 176: retrieving length without query sequence ... ok testPositions (AlignedSegment_test.TestAlignedSegment) ... ok see issue 62 ... ok testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok testAsString (AlignedSegment_test.TestAsString) ... ok testStats (AlignedSegment_test.TestCigarStats) ... ok testCopy (AlignedSegment_test.TestCopy) ... ok testDeepCopy (AlignedSegment_test.TestCopy) ... ok testAddTags (AlignedSegment_test.TestTags) ... ok testAddTagsType (AlignedSegment_test.TestTags) ... ok testArrayTags (AlignedSegment_test.TestTags) ... ok testEmptyTag (AlignedSegment_test.TestTags) ... ok testMDTagComplex (AlignedSegment_test.TestTags) ... ok testMDTagDeletions (AlignedSegment_test.TestTags) ... ok testMDTagInsertions (AlignedSegment_test.TestTags) ... ok testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok testMissingTag (AlignedSegment_test.TestTags) ... ok testSetTag (AlignedSegment_test.TestTags) ... ok test for tag parsing ... ok testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testRaises (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testTags (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testIndex (AlignmentFile_test.TestAlignmentFileIndex) ... ok testCount (AlignmentFile_test.TestAlignmentFileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok test BAM autodetection. ... ok test CRAM autodetection. ... ok test SAM autodetection. ... ok testReadTags (AlignmentFile_test.TestBTagBam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagBam) ... ok testReadTags (AlignmentFile_test.TestBTagSam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagSam) ... ok testClipping (AlignmentFile_test.TestClipping) ... ok testManager (AlignmentFile_test.TestContextManager) ... ok test_count_coverage (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_nofilter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_quality_filter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_all (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_callback (AlignmentFile_test.TestCountCoverage) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testEmptyHeader (AlignmentFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (AlignmentFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (AlignmentFile_test.TestExceptions) ... ok testBadContig (AlignmentFile_test.TestExceptions) ... ok testMeaninglessCrap (AlignmentFile_test.TestExceptions) ... ok testMissingFile (AlignmentFile_test.TestExceptions) ... ok testOutOfRangNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (AlignmentFile_test.TestExceptions) ... ok see issue 44 ... ok testExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... Warning: The index file is older than the data file: /<>/python-pysam-0.10.0+ds/tests/pysam_data/ex1.bam.bai ok testExplicitIndexCRAM (AlignmentFile_test.TestExplicitIndex) ... ok testRemoteExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... ok test_all (AlignmentFile_test.TestFindIntrons) ... ok test_first (AlignmentFile_test.TestFindIntrons) ... ok test_total (AlignmentFile_test.TestFindIntrons) ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (AlignmentFile_test.TestHeader1000Genomes) ... ok testHeaders (AlignmentFile_test.TestHeaderBAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderBAM) ... ok testHeaders (AlignmentFile_test.TestHeaderCRAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderCRAM) ... ok testHeaders (AlignmentFile_test.TestHeaderSAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderSAM) ... ok testHeader (AlignmentFile_test.TestHeaderWithProgramOptions) ... ok test_BAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_CRAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_SAM (AlignmentFile_test.TestHeaderWriteRead) ... ok testBAM2BAM (AlignmentFile_test.TestIO) ... ok testBAM2CRAM (AlignmentFile_test.TestIO) ... ok testBAM2SAM (AlignmentFile_test.TestIO) ... ok see issue 116 ... ok see issue 116 ... ok see issue 117 ... ok testCRAM2BAM (AlignmentFile_test.TestIO) ... ok testCRAM2CRAM (AlignmentFile_test.TestIO) ... ok testCRAM2SAM (AlignmentFile_test.TestIO) ... ok test that access to a closed samfile raises ValueError. ... ok testEmptyBAM (AlignmentFile_test.TestIO) ... ok testEmptyWithHeaderBAM (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFile (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFileObject (AlignmentFile_test.TestIO) ... ok test IteratorRowHead ... ok testOpenFromFilename (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok testReadSamWithoutHeader (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok read from bam file without index. ... ok testSAM2BAM (AlignmentFile_test.TestIO) ... ok testSAM2CRAM (AlignmentFile_test.TestIO) ... ok testSAM2SAM (AlignmentFile_test.TestIO) ... ok testSAM2SAMWithoutHeader (AlignmentFile_test.TestIO) ... ok read from uncompressed BAM file, see issue #43 ... ok see issue 131 ... ok testStart (AlignmentFile_test.TestIteratorColumn2) ... ok test if PileupRead can be printed. ... ok see issue 107. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok when creating a read with a large entry in the tag field ... ok testBAM (AlignmentFile_test.TestLargeOptValues) ... ok testSAM (AlignmentFile_test.TestLargeOptValues) ... ok testFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail2 (AlignmentFile_test.TestLogging) ... ok testMapped (AlignmentFile_test.TestMappedUnmapped) ... ok testAllStepper (AlignmentFile_test.TestPileup) ... ok testSamtoolsStepper (AlignmentFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (AlignmentFile_test.TestPileupObjects) ... ok testPileupRead (AlignmentFile_test.TestPileupObjects) ... ok testPileup (AlignmentFile_test.TestPileupQueryPosition) ... ok testFTPFetch (AlignmentFile_test.TestRemoteFileFTP) ... ok testFTPView (AlignmentFile_test.TestRemoteFileFTP) ... ok testFetch (AlignmentFile_test.TestRemoteFileHTTP) ... ok testFetchAll (AlignmentFile_test.TestRemoteFileHTTP) ... ok testView (AlignmentFile_test.TestRemoteFileHTTP) ... ok testIndex (AlignmentFile_test.TestSamtoolsProxy) ... ok testSort (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok test_empty_read_gives_value_error (AlignmentFile_test.TestSanityCheckingBAM) ... ok testArrayTags (AlignmentFile_test.TestTagParsing) ... ok testCigar (AlignmentFile_test.TestTagParsing) ... ok testCigarString (AlignmentFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (AlignmentFile_test.TestTagParsing) ... ok testNegativeIntegers2 (AlignmentFile_test.TestTagParsing) ... ok testTruncatedBam (AlignmentFile_test.TestTruncatedBAM) ... [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. [E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes ok See comments for pull request at ... ok testBAM (AlignmentFile_test.TestUnmappedReads) ... ok testVerbosity (AlignmentFile_test.TestVerbosity) ... ok testOpenBamAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenSamAsBam (AlignmentFile_test.TestWrongFormat) ... ok testARcigar (SamFile_test.BasicTestBAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestBAMFetch) ... ok testARflag (SamFile_test.BasicTestBAMFetch) ... ok testARisize (SamFile_test.BasicTestBAMFetch) ... ok testARmapq (SamFile_test.BasicTestBAMFetch) ... ok testARmpos (SamFile_test.BasicTestBAMFetch) ... ok testARmrnm (SamFile_test.BasicTestBAMFetch) ... ok testARpos (SamFile_test.BasicTestBAMFetch) ... ok testARqname (SamFile_test.BasicTestBAMFetch) ... ok testARqqual (SamFile_test.BasicTestBAMFetch) ... ok testARqual (SamFile_test.BasicTestBAMFetch) ... ok testARquery (SamFile_test.BasicTestBAMFetch) ... ok testARrname (SamFile_test.BasicTestBAMFetch) ... ok testARseq (SamFile_test.BasicTestBAMFetch) ... ok testAddTags (SamFile_test.BasicTestBAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestBAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestBAMFetch) ... ok testOpt (SamFile_test.BasicTestBAMFetch) ... ok testPairedBools (SamFile_test.BasicTestBAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFetch) ... ok testTags (SamFile_test.BasicTestBAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFetch) ... ok testARcigar (SamFile_test.BasicTestBAMFile) ... ok testARcigarstring (SamFile_test.BasicTestBAMFile) ... ok testARflag (SamFile_test.BasicTestBAMFile) ... ok testARisize (SamFile_test.BasicTestBAMFile) ... ok testARmapq (SamFile_test.BasicTestBAMFile) ... ok testARmpos (SamFile_test.BasicTestBAMFile) ... ok testARmrnm (SamFile_test.BasicTestBAMFile) ... ok testARpos (SamFile_test.BasicTestBAMFile) ... ok testARqname (SamFile_test.BasicTestBAMFile) ... ok testARqqual (SamFile_test.BasicTestBAMFile) ... ok testARqual (SamFile_test.BasicTestBAMFile) ... ok testARquery (SamFile_test.BasicTestBAMFile) ... ok testARrname (SamFile_test.BasicTestBAMFile) ... ok testARseq (SamFile_test.BasicTestBAMFile) ... ok testAddTags (SamFile_test.BasicTestBAMFile) ... ok testAddTagsType (SamFile_test.BasicTestBAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFile) ... ok testMissingOpt (SamFile_test.BasicTestBAMFile) ... ok testOpt (SamFile_test.BasicTestBAMFile) ... ok testPairedBools (SamFile_test.BasicTestBAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFile) ... ok testTags (SamFile_test.BasicTestBAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFile) ... ok testARcigar (SamFile_test.BasicTestSAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestSAMFetch) ... ok testARflag (SamFile_test.BasicTestSAMFetch) ... ok testARisize (SamFile_test.BasicTestSAMFetch) ... ok testARmapq (SamFile_test.BasicTestSAMFetch) ... ok testARmpos (SamFile_test.BasicTestSAMFetch) ... ok testARmrnm (SamFile_test.BasicTestSAMFetch) ... ok testARpos (SamFile_test.BasicTestSAMFetch) ... ok testARqname (SamFile_test.BasicTestSAMFetch) ... ok testARqqual (SamFile_test.BasicTestSAMFetch) ... ok testARqual (SamFile_test.BasicTestSAMFetch) ... ok testARquery (SamFile_test.BasicTestSAMFetch) ... ok testARrname (SamFile_test.BasicTestSAMFetch) ... ok testARseq (SamFile_test.BasicTestSAMFetch) ... ok testAddTags (SamFile_test.BasicTestSAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestSAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestSAMFetch) ... ok testOpt (SamFile_test.BasicTestSAMFetch) ... ok testPairedBools (SamFile_test.BasicTestSAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFetch) ... ok testTags (SamFile_test.BasicTestSAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFetch) ... ok testARcigar (SamFile_test.BasicTestSAMFile) ... ok testARcigarstring (SamFile_test.BasicTestSAMFile) ... ok testARflag (SamFile_test.BasicTestSAMFile) ... ok testARisize (SamFile_test.BasicTestSAMFile) ... ok testARmapq (SamFile_test.BasicTestSAMFile) ... ok testARmpos (SamFile_test.BasicTestSAMFile) ... ok testARmrnm (SamFile_test.BasicTestSAMFile) ... ok testARpos (SamFile_test.BasicTestSAMFile) ... ok testARqname (SamFile_test.BasicTestSAMFile) ... ok testARqqual (SamFile_test.BasicTestSAMFile) ... ok testARqual (SamFile_test.BasicTestSAMFile) ... ok testARquery (SamFile_test.BasicTestSAMFile) ... ok testARrname (SamFile_test.BasicTestSAMFile) ... ok testARseq (SamFile_test.BasicTestSAMFile) ... ok testAddTags (SamFile_test.BasicTestSAMFile) ... ok testAddTagsType (SamFile_test.BasicTestSAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFile) ... ok testMissingOpt (SamFile_test.BasicTestSAMFile) ... ok testOpt (SamFile_test.BasicTestSAMFile) ... ok testPairedBools (SamFile_test.BasicTestSAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFile) ... ok testTags (SamFile_test.BasicTestSAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFile) ... ok testBlocks (SamFile_test.TestAlignedRead) ... ok testEmpty (SamFile_test.TestAlignedRead) ... ok build an example read. ... ok testPositions (SamFile_test.TestAlignedRead) ... ok testStrOfEmptyRead (SamFile_test.TestAlignedRead) ... ok test for tag parsing ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok testReadTags (SamFile_test.TestBTagBam) ... ok testReadWriteTags (SamFile_test.TestBTagBam) ... ok testReadTags (SamFile_test.TestBTagSam) ... ok testReadWriteTags (SamFile_test.TestBTagSam) ... ok testClipping (SamFile_test.TestClipping) ... ok testManager (SamFile_test.TestContextManager) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchUntilEOF (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchWithRegion (SamFile_test.TestDoubleFetch) ... ok testEmptyHeader (SamFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (SamFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (SamFile_test.TestExceptions) ... ok testBadContig (SamFile_test.TestExceptions) ... ok testMeaninglessCrap (SamFile_test.TestExceptions) ... ok testMissingFile (SamFile_test.TestExceptions) ... ok testOutOfRangNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (SamFile_test.TestExceptions) ... ok see issue 44 ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (SamFile_test.TestHeader1000Genomes) ... ok testHeaders (SamFile_test.TestHeaderBam) ... ok testNameMapping (SamFile_test.TestHeaderBam) ... ok testHeaders (SamFile_test.TestHeaderSam) ... ok testNameMapping (SamFile_test.TestHeaderSam) ... ok test if autodetection works. ... ok see issue 116 ... ok see issue 117 ... ok test that access to a closed samfile raises ValueError. ... ok testFetchFromClosedFile (SamFile_test.TestIO) ... ok test IteratorRowHead ... ok see issue 104. ... ok testReadSamWithoutHeader (SamFile_test.TestIO) ... ok see issue 104. ... ok testReadWriteBam (SamFile_test.TestIO) ... ok testReadWriteSamWithHeader (SamFile_test.TestIO) ... ok testReadWriteSamWithoutHeader (SamFile_test.TestIO) ... ok read from bam file without index. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok see issue 131 ... ok testStart (SamFile_test.TestIteratorColumn2) ... ok see issue 107. ... ok check random access per contig ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok when creating a read with a large entry in the tag field ... ok testBAM (SamFile_test.TestLargeOptValues) ... ok testSAM (SamFile_test.TestLargeOptValues) ... ok testFail1 (SamFile_test.TestLogging) ... ok testNoFail1 (SamFile_test.TestLogging) ... ok testNoFail2 (SamFile_test.TestLogging) ... ok testAllStepper (SamFile_test.TestPileup) ... ok testSamtoolsStepper (SamFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (SamFile_test.TestPileupObjects) ... ok testPileupRead (SamFile_test.TestPileupObjects) ... ok testFTPFetch (SamFile_test.TestRemoteFileFTP) ... ok testFTPView (SamFile_test.TestRemoteFileFTP) ... ok testFetch (SamFile_test.TestRemoteFileHTTP) ... ok testFetchAll (SamFile_test.TestRemoteFileHTTP) ... ok testView (SamFile_test.TestRemoteFileHTTP) ... ok testIndex (SamFile_test.TestSamfileIndex) ... ok testCount (SamFile_test.TestSamfileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok testIndex (SamFile_test.TestSamtoolsProxy) ... ok testSort (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testCigar (SamFile_test.TestTagParsing) ... ok testCigarString (SamFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (SamFile_test.TestTagParsing) ... ok testNegativeIntegers2 (SamFile_test.TestTagParsing) ... ok testBAM (SamFile_test.TestUnmappedReads) ... ok testOpenBamAsSam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (SamFile_test.TestWrongFormat) ... ok testOpenSamAsBam (SamFile_test.TestWrongFormat) ... ok test_samtools_processing (StreamFiledescriptors_test.StreamTest) ... ok test_text_processing (StreamFiledescriptors_test.StreamTest) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testBase (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFWithContigs) ... ok testIterator (VariantFile_test.TestHeader) ... ok testStr (VariantFile_test.TestHeader) ... ok testOpen (VariantFile_test.TestIndexFilename) ... ok testVCF (VariantFile_test.TestMissingGenotypes) ... ok testVCFGZ (VariantFile_test.TestMissingGenotypes) ... ok testDetectBCF (VariantFile_test.TestOpening) ... ok testDetectVCF (VariantFile_test.TestOpening) ... [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.) ok testDetectVCFGZ (VariantFile_test.TestOpening) ... ok testEmptyFileVCF (VariantFile_test.TestOpening) ... ok testEmptyFileVCFFromPath (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZOnlyHeader (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithoutIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFOnlyHeader (VariantFile_test.TestOpening) ... ok testMissingFile (VariantFile_test.TestOpening) ... ok testMissingFileVCFGZ (VariantFile_test.TestOpening) ... ok testAlleles (VariantFile_test.TestParsing) ... ok testAlt (VariantFile_test.TestParsing) ... ok testChrom (VariantFile_test.TestParsing) ... ok testChromFromPath (VariantFile_test.TestParsing) ... ok testFilter (VariantFile_test.TestParsing) ... ok testFormat (VariantFile_test.TestParsing) ... ok testId (VariantFile_test.TestParsing) ... ok testInfo (VariantFile_test.TestParsing) ... ok testPos (VariantFile_test.TestParsing) ... ok testQual (VariantFile_test.TestParsing) ... ok testRef (VariantFile_test.TestParsing) ... ok testSampleAlleleIndices (VariantFile_test.TestParsing) ... ok testSampleAlleles (VariantFile_test.TestParsing) ... ok testSampleFormats (VariantFile_test.TestParsing) ... ok testStart (VariantFile_test.TestParsing) ... ok testStop (VariantFile_test.TestParsing) ... ok testBase (VariantFile_test.TestSettingRecordValues) ... ok testGenotype (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSetQual (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSubsetting (VariantFile_test.TestSubsetting) ... In file included from /<>/python-pysam-0.10.0+ds/tests/_compile_test.c:439:0: /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ ok testCount (compile_test.BAMTest) ... ok testCount (compile_test.GTFTest) ... ok testFetch (faidx_test.TestFastaFile) ... ok testFetchErrors (faidx_test.TestFastaFile) ... ok testLength (faidx_test.TestFastaFile) ... ok test out of range access. ... ok testSequenceLengths (faidx_test.TestFastaFile) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndex) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testCounts (faidx_test.TestFastqFileFastq) ... ok testManager (faidx_test.TestFastqFileFastq) ... ok testMissingFile (faidx_test.TestFastqFileFastq) ... ok testSequence (faidx_test.TestFastqFileFastq) ... ok testCounts (faidx_test.TestFastxFileFasta) ... ok testManager (faidx_test.TestFastxFileFasta) ... ok testMissingFile (faidx_test.TestFastxFileFasta) ... ok testSequence (faidx_test.TestFastxFileFasta) ... ok testCounts (faidx_test.TestFastxFileFastq) ... ok testManager (faidx_test.TestFastxFileFastq) ... ok testMissingFile (faidx_test.TestFastxFileFastq) ... ok testSequence (faidx_test.TestFastxFileFastq) ... ok testCounts (faidx_test.TestFastxFileFastqStream) ... ok testManager (faidx_test.TestFastxFileFastqStream) ... ok testMissingFile (faidx_test.TestFastxFileFastqStream) ... ok testSequence (faidx_test.TestFastxFileFastqStream) ... ok testIteration (faidx_test.TestFastxFileWithEmptySequence) ... ok testStatements (samtools_test.BcftoolsTest) ... [W::bcf_hdr_check_sanity] GL should be declared as Number=G ok testEmptyIndex (samtools_test.EmptyIndexTest) ... ok testStatements (samtools_test.PysamTest) ... ok testStatements (samtools_test.SamtoolsTest) ... ok testDoubleCalling (samtools_test.StdoutTest) ... ok testSaveStdout (samtools_test.StdoutTest) ... ok testWithRedirectedStdout (samtools_test.StdoutTest) ... ok testWithoutRedirectedStdout (samtools_test.StdoutTest) ... ok testReturnValueData (samtools_test.TestReturnType) ... ok testReturnValueString (samtools_test.TestReturnType) ... ok testBED (tabix_test.TestBackwardsCompatibility) ... ok testBED0v23 (tabix_test.TestBackwardsCompatibility) ... ok testBED0v26 (tabix_test.TestBackwardsCompatibility) ... ok testEmpty (tabix_test.TestBackwardsCompatibility) ... ok testVCF (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v23 (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v26 (tabix_test.TestBackwardsCompatibility) ... ok testRead (tabix_test.TestBed) ... ok testWrite (tabix_test.TestBed) ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok testManager (tabix_test.TestContextManager) ... ok testCopy (tabix_test.TestGTF) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestGTF) ... ok testSetting (tabix_test.TestGTF) ... ok testUnset (tabix_test.TestGTF) ... ok testWrite (tabix_test.TestGTF) ... ok testAll (tabix_test.TestGZFile) ... ok testFetchAll (tabix_test.TestIndexArgument) ... ok test indexing via preset. ... ok testGTFTooFewFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testGTFTooManyFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testAll (tabix_test.TestIterationWithComments) ... ok testGetContigs (tabix_test.TestIterationWithComments) ... ok testHeader (tabix_test.TestIterationWithComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithComments) ... ok testPerContig (tabix_test.TestIterationWithComments) ... ok testPerContig2 (tabix_test.TestIterationWithComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithComments) ... ok testPerInterval (tabix_test.TestIterationWithComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok testAll (tabix_test.TestIterationWithoutComments) ... ok testGetContigs (tabix_test.TestIterationWithoutComments) ... ok testHeader (tabix_test.TestIterationWithoutComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithoutComments) ... ok testPerContig (tabix_test.TestIterationWithoutComments) ... ok testPerContig2 (tabix_test.TestIterationWithoutComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithoutComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithoutComments) ... ok testPerInterval (tabix_test.TestIterationWithoutComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIterators) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileCompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileUncompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsGenericCompressed) ... ok testDisjointIterators (tabix_test.TestMultipleIterators) ... ok testDoubleFetch (tabix_test.TestMultipleIterators) ... ok testJoinedIterators (tabix_test.TestMultipleIterators) ... ok testScope (tabix_test.TestMultipleIterators) ... ok testCopy (tabix_test.TestParser) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestParser) ... ok testUnset (tabix_test.TestParser) ... ok testWrite (tabix_test.TestParser) ... ok testFetchAll (tabix_test.TestRemoteFileHTTP) ... ok testHeader (tabix_test.TestRemoteFileHTTP) ... ok testFromTabix (tabix_test.TestUnicode) ... ok testFromVCF (tabix_test.TestUnicode) ... ok testRead (tabix_test.TestVCFFromTabix) ... ok testWrite (tabix_test.TestVCFFromTabix) ... ok testConnecting (tabix_test.TestVCFFromVCF) ... ok testParsing (tabix_test.TestVCFFromVCF) ... ok testConnecting (tabix_test.TestVCFFromVariantFile) ... ok testParsing (tabix_test.TestVCFFromVariantFile) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_10) ... ok testParsing (tabix_test.TestVCFFromVariantFile_10) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_11) ... ok testParsing (tabix_test.TestVCFFromVariantFile_11) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_12) ... ok testParsing (tabix_test.TestVCFFromVariantFile_12) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_13) ... ok testParsing (tabix_test.TestVCFFromVariantFile_13) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_15) ... ok testParsing (tabix_test.TestVCFFromVariantFile_15) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_16) ... ok testParsing (tabix_test.TestVCFFromVariantFile_16) ... [W::bcf_hdr_check_sanity] PL should be declared as Number=G [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_18) ... ok testParsing (tabix_test.TestVCFFromVariantFile_18) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_2) ... ok testParsing (tabix_test.TestVCFFromVariantFile_2) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_20) ... ok testParsing (tabix_test.TestVCFFromVariantFile_20) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_21) ... ok testParsing (tabix_test.TestVCFFromVariantFile_21) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_22) ... ok testParsing (tabix_test.TestVCFFromVariantFile_22) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_23) ... ok testParsing (tabix_test.TestVCFFromVariantFile_23) ... [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_24) ... ok testParsing (tabix_test.TestVCFFromVariantFile_24) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_3) ... ok testParsing (tabix_test.TestVCFFromVariantFile_3) ... [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_4) ... ok testParsing (tabix_test.TestVCFFromVariantFile_4) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_5) ... ok testParsing (tabix_test.TestVCFFromVariantFile_5) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_6) ... ok testParsing (tabix_test.TestVCFFromVariantFile_6) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_7) ... ok testParsing (tabix_test.TestVCFFromVariantFile_7) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_8) ... ok testParsing (tabix_test.TestVCFFromVariantFile_8) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_9) ... ok testParsing (tabix_test.TestVCFFromVariantFile_9) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_issue85) ... ok testParsing (tabix_test.TestVCFFromVariantFile_issue85) ... ok testConnecting (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testParsing (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testRead (tabix_test.VCFFromTabixTest_10) ... ok testWrite (tabix_test.VCFFromTabixTest_10) ... ok testRead (tabix_test.VCFFromTabixTest_11) ... ok testWrite (tabix_test.VCFFromTabixTest_11) ... ok testRead (tabix_test.VCFFromTabixTest_12) ... ok testWrite (tabix_test.VCFFromTabixTest_12) ... ok testRead (tabix_test.VCFFromTabixTest_13) ... ok testWrite (tabix_test.VCFFromTabixTest_13) ... ok testRead (tabix_test.VCFFromTabixTest_15) ... ok testWrite (tabix_test.VCFFromTabixTest_15) ... ok testRead (tabix_test.VCFFromTabixTest_16) ... ok testWrite (tabix_test.VCFFromTabixTest_16) ... ok testRead (tabix_test.VCFFromTabixTest_18) ... ok testWrite (tabix_test.VCFFromTabixTest_18) ... ok testRead (tabix_test.VCFFromTabixTest_2) ... ok testWrite (tabix_test.VCFFromTabixTest_2) ... ok testRead (tabix_test.VCFFromTabixTest_20) ... ok testWrite (tabix_test.VCFFromTabixTest_20) ... ok testRead (tabix_test.VCFFromTabixTest_21) ... ok testWrite (tabix_test.VCFFromTabixTest_21) ... ok testRead (tabix_test.VCFFromTabixTest_22) ... ok testWrite (tabix_test.VCFFromTabixTest_22) ... ok testRead (tabix_test.VCFFromTabixTest_23) ... ok testWrite (tabix_test.VCFFromTabixTest_23) ... ok testRead (tabix_test.VCFFromTabixTest_24) ... ok testWrite (tabix_test.VCFFromTabixTest_24) ... ok testRead (tabix_test.VCFFromTabixTest_3) ... ok testWrite (tabix_test.VCFFromTabixTest_3) ... ok testRead (tabix_test.VCFFromTabixTest_4) ... ok testWrite (tabix_test.VCFFromTabixTest_4) ... ok testRead (tabix_test.VCFFromTabixTest_5) ... ok testWrite (tabix_test.VCFFromTabixTest_5) ... ok testRead (tabix_test.VCFFromTabixTest_6) ... ok testWrite (tabix_test.VCFFromTabixTest_6) ... ok testRead (tabix_test.VCFFromTabixTest_7) ... ok testWrite (tabix_test.VCFFromTabixTest_7) ... ok testRead (tabix_test.VCFFromTabixTest_8) ... ok testWrite (tabix_test.VCFFromTabixTest_8) ... ok testRead (tabix_test.VCFFromTabixTest_9) ... ok testWrite (tabix_test.VCFFromTabixTest_9) ... ok testRead (tabix_test.VCFFromTabixTest_issue85) ... ok testWrite (tabix_test.VCFFromTabixTest_issue85) ... ok testRead (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testWrite (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testConnecting (tabix_test.VCFFromVCFTest_10) ... ok testParsing (tabix_test.VCFFromVCFTest_10) ... ok testConnecting (tabix_test.VCFFromVCFTest_11) ... ok testParsing (tabix_test.VCFFromVCFTest_11) ... ok testConnecting (tabix_test.VCFFromVCFTest_12) ... ok testParsing (tabix_test.VCFFromVCFTest_12) ... ok testConnecting (tabix_test.VCFFromVCFTest_13) ... ok testParsing (tabix_test.VCFFromVCFTest_13) ... ok testConnecting (tabix_test.VCFFromVCFTest_15) ... ok testParsing (tabix_test.VCFFromVCFTest_15) ... ok testConnecting (tabix_test.VCFFromVCFTest_16) ... ok testParsing (tabix_test.VCFFromVCFTest_16) ... ok testConnecting (tabix_test.VCFFromVCFTest_18) ... ok testParsing (tabix_test.VCFFromVCFTest_18) ... ok testConnecting (tabix_test.VCFFromVCFTest_2) ... ok testParsing (tabix_test.VCFFromVCFTest_2) ... ok testConnecting (tabix_test.VCFFromVCFTest_20) ... ok testParsing (tabix_test.VCFFromVCFTest_20) ... ok testConnecting (tabix_test.VCFFromVCFTest_21) ... ok testParsing (tabix_test.VCFFromVCFTest_21) ... ok testConnecting (tabix_test.VCFFromVCFTest_22) ... ok testParsing (tabix_test.VCFFromVCFTest_22) ... ok testConnecting (tabix_test.VCFFromVCFTest_23) ... ok testParsing (tabix_test.VCFFromVCFTest_23) ... ok testConnecting (tabix_test.VCFFromVCFTest_24) ... ok testParsing (tabix_test.VCFFromVCFTest_24) ... ok testConnecting (tabix_test.VCFFromVCFTest_3) ... ok testParsing (tabix_test.VCFFromVCFTest_3) ... ok testConnecting (tabix_test.VCFFromVCFTest_4) ... ok testParsing (tabix_test.VCFFromVCFTest_4) ... ok testConnecting (tabix_test.VCFFromVCFTest_5) ... ok testParsing (tabix_test.VCFFromVCFTest_5) ... ok testConnecting (tabix_test.VCFFromVCFTest_6) ... ok testParsing (tabix_test.VCFFromVCFTest_6) ... ok testConnecting (tabix_test.VCFFromVCFTest_7) ... ok testParsing (tabix_test.VCFFromVCFTest_7) ... ok testConnecting (tabix_test.VCFFromVCFTest_8) ... ok testParsing (tabix_test.VCFFromVCFTest_8) ... ok testConnecting (tabix_test.VCFFromVCFTest_9) ... ok testParsing (tabix_test.VCFFromVCFTest_9) ... ok testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok test_samtools_python.test_idxstats_parse_split_lines ... ok test_samtools_python.test_bedcov_split_lines ... ok test_samtools_python.test_idxstats_parse ... ok test_samtools_python.test_bedcov ... ok ---------------------------------------------------------------------- Ran 919 tests in 246.300s OK (0, 0) I: pybuild base:184: cd /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose reference bases should always be the same nucleotide ... ok testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok check comparison functions. ... ok testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok see issue 26 ... ok testHashing (AlignedSegment_test.TestAlignedSegment) ... ok build an example read. ... ok issue 176: retrieving length without query sequence ... ok testPositions (AlignedSegment_test.TestAlignedSegment) ... ok see issue 62 ... ok testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok testAsString (AlignedSegment_test.TestAsString) ... ok testStats (AlignedSegment_test.TestCigarStats) ... ok testCopy (AlignedSegment_test.TestCopy) ... ok testDeepCopy (AlignedSegment_test.TestCopy) ... ok testAddTags (AlignedSegment_test.TestTags) ... ok testAddTagsType (AlignedSegment_test.TestTags) ... ok testArrayTags (AlignedSegment_test.TestTags) ... ok testEmptyTag (AlignedSegment_test.TestTags) ... ok testMDTagComplex (AlignedSegment_test.TestTags) ... ok testMDTagDeletions (AlignedSegment_test.TestTags) ... ok testMDTagInsertions (AlignedSegment_test.TestTags) ... ok testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok testMissingTag (AlignedSegment_test.TestTags) ... ok testSetTag (AlignedSegment_test.TestTags) ... ok test for tag parsing ... ok testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFetch) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFile) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFile) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFile) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFile) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testTags (AlignmentFile_test.BasicTestSAMFromFilename) ... ok testARQueryLength (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigar (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARcigarstring (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARflag (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmapq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARmrnm (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARquery (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARrname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testARseq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testOpt (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPairedBools (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testRaises (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testTags (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok testIndex (AlignmentFile_test.TestAlignmentFileIndex) ... ok testCount (AlignmentFile_test.TestAlignmentFileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok test BAM autodetection. ... ok test CRAM autodetection. ... ok test SAM autodetection. ... ok testReadTags (AlignmentFile_test.TestBTagBam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagBam) ... ok testReadTags (AlignmentFile_test.TestBTagSam) ... ok testReadWriteTags (AlignmentFile_test.TestBTagSam) ... ok testClipping (AlignmentFile_test.TestClipping) ... ok testManager (AlignmentFile_test.TestContextManager) ... ok test_count_coverage (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_nofilter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_quality_filter (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_all (AlignmentFile_test.TestCountCoverage) ... ok test_count_coverage_read_callback (AlignmentFile_test.TestCountCoverage) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (AlignmentFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchBAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAM) ... ok testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok testEmptyHeader (AlignmentFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (AlignmentFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (AlignmentFile_test.TestExceptions) ... ok testBadContig (AlignmentFile_test.TestExceptions) ... ok testMeaninglessCrap (AlignmentFile_test.TestExceptions) ... ok testMissingFile (AlignmentFile_test.TestExceptions) ... ok testOutOfRangNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (AlignmentFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (AlignmentFile_test.TestExceptions) ... ok see issue 44 ... ok testExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... Warning: The index file is older than the data file: /<>/python-pysam-0.10.0+ds/tests/pysam_data/ex1.bam.bai ok testExplicitIndexCRAM (AlignmentFile_test.TestExplicitIndex) ... ok testRemoteExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... ok test_all (AlignmentFile_test.TestFindIntrons) ... ok test_first (AlignmentFile_test.TestFindIntrons) ... ok test_total (AlignmentFile_test.TestFindIntrons) ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (AlignmentFile_test.TestHeader1000Genomes) ... ok testHeaders (AlignmentFile_test.TestHeaderBAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderBAM) ... ok testHeaders (AlignmentFile_test.TestHeaderCRAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderCRAM) ... ok testHeaders (AlignmentFile_test.TestHeaderSAM) ... ok testNameMapping (AlignmentFile_test.TestHeaderSAM) ... ok testHeader (AlignmentFile_test.TestHeaderWithProgramOptions) ... ok test_BAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_CRAM (AlignmentFile_test.TestHeaderWriteRead) ... ok test_SAM (AlignmentFile_test.TestHeaderWriteRead) ... ok testBAM2BAM (AlignmentFile_test.TestIO) ... ok testBAM2CRAM (AlignmentFile_test.TestIO) ... ok testBAM2SAM (AlignmentFile_test.TestIO) ... ok see issue 116 ... ok see issue 116 ... ok see issue 117 ... ok testCRAM2BAM (AlignmentFile_test.TestIO) ... ok testCRAM2CRAM (AlignmentFile_test.TestIO) ... ok testCRAM2SAM (AlignmentFile_test.TestIO) ... ok test that access to a closed samfile raises ValueError. ... ok testEmptyBAM (AlignmentFile_test.TestIO) ... ok testEmptyWithHeaderBAM (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFile (AlignmentFile_test.TestIO) ... ok testFetchFromClosedFileObject (AlignmentFile_test.TestIO) ... ok test IteratorRowHead ... ok testOpenFromFilename (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok testReadSamWithoutHeader (AlignmentFile_test.TestIO) ... ok see issue 104. ... ok read from bam file without index. ... ok testSAM2BAM (AlignmentFile_test.TestIO) ... ok testSAM2CRAM (AlignmentFile_test.TestIO) ... ok testSAM2SAM (AlignmentFile_test.TestIO) ... ok testSAM2SAMWithoutHeader (AlignmentFile_test.TestIO) ... ok read from uncompressed BAM file, see issue #43 ... ok see issue 131 ... ok testStart (AlignmentFile_test.TestIteratorColumn2) ... ok test if PileupRead can be printed. ... ok see issue 107. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok check random access per contig ... ok check random access per range ... ok when creating a read with a large entry in the tag field ... ok testBAM (AlignmentFile_test.TestLargeOptValues) ... ok testSAM (AlignmentFile_test.TestLargeOptValues) ... ok testFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail1 (AlignmentFile_test.TestLogging) ... ok testNoFail2 (AlignmentFile_test.TestLogging) ... ok testMapped (AlignmentFile_test.TestMappedUnmapped) ... ok testAllStepper (AlignmentFile_test.TestPileup) ... ok testSamtoolsStepper (AlignmentFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (AlignmentFile_test.TestPileupObjects) ... ok testPileupRead (AlignmentFile_test.TestPileupObjects) ... ok testPileup (AlignmentFile_test.TestPileupQueryPosition) ... ok testFTPFetch (AlignmentFile_test.TestRemoteFileFTP) ... ok testFTPView (AlignmentFile_test.TestRemoteFileFTP) ... ok testFetch (AlignmentFile_test.TestRemoteFileHTTP) ... ok testFetchAll (AlignmentFile_test.TestRemoteFileHTTP) ... ok testView (AlignmentFile_test.TestRemoteFileHTTP) ... ok testIndex (AlignmentFile_test.TestSamtoolsProxy) ... ok testSort (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok test_empty_read_gives_value_error (AlignmentFile_test.TestSanityCheckingBAM) ... ok testArrayTags (AlignmentFile_test.TestTagParsing) ... ok testCigar (AlignmentFile_test.TestTagParsing) ... ok testCigarString (AlignmentFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (AlignmentFile_test.TestTagParsing) ... ok testNegativeIntegers2 (AlignmentFile_test.TestTagParsing) ... ok testTruncatedBam (AlignmentFile_test.TestTruncatedBAM) ... [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. [E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes ok See comments for pull request at ... ok testBAM (AlignmentFile_test.TestUnmappedReads) ... ok testVerbosity (AlignmentFile_test.TestVerbosity) ... ok testOpenBamAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (AlignmentFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (AlignmentFile_test.TestWrongFormat) ... ok testOpenSamAsBam (AlignmentFile_test.TestWrongFormat) ... ok testARcigar (SamFile_test.BasicTestBAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestBAMFetch) ... ok testARflag (SamFile_test.BasicTestBAMFetch) ... ok testARisize (SamFile_test.BasicTestBAMFetch) ... ok testARmapq (SamFile_test.BasicTestBAMFetch) ... ok testARmpos (SamFile_test.BasicTestBAMFetch) ... ok testARmrnm (SamFile_test.BasicTestBAMFetch) ... ok testARpos (SamFile_test.BasicTestBAMFetch) ... ok testARqname (SamFile_test.BasicTestBAMFetch) ... ok testARqqual (SamFile_test.BasicTestBAMFetch) ... ok testARqual (SamFile_test.BasicTestBAMFetch) ... ok testARquery (SamFile_test.BasicTestBAMFetch) ... ok testARrname (SamFile_test.BasicTestBAMFetch) ... ok testARseq (SamFile_test.BasicTestBAMFetch) ... ok testAddTags (SamFile_test.BasicTestBAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestBAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestBAMFetch) ... ok testOpt (SamFile_test.BasicTestBAMFetch) ... ok testPairedBools (SamFile_test.BasicTestBAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFetch) ... ok testTags (SamFile_test.BasicTestBAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFetch) ... ok testARcigar (SamFile_test.BasicTestBAMFile) ... ok testARcigarstring (SamFile_test.BasicTestBAMFile) ... ok testARflag (SamFile_test.BasicTestBAMFile) ... ok testARisize (SamFile_test.BasicTestBAMFile) ... ok testARmapq (SamFile_test.BasicTestBAMFile) ... ok testARmpos (SamFile_test.BasicTestBAMFile) ... ok testARmrnm (SamFile_test.BasicTestBAMFile) ... ok testARpos (SamFile_test.BasicTestBAMFile) ... ok testARqname (SamFile_test.BasicTestBAMFile) ... ok testARqqual (SamFile_test.BasicTestBAMFile) ... ok testARqual (SamFile_test.BasicTestBAMFile) ... ok testARquery (SamFile_test.BasicTestBAMFile) ... ok testARrname (SamFile_test.BasicTestBAMFile) ... ok testARseq (SamFile_test.BasicTestBAMFile) ... ok testAddTags (SamFile_test.BasicTestBAMFile) ... ok testAddTagsType (SamFile_test.BasicTestBAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestBAMFile) ... ok testMissingOpt (SamFile_test.BasicTestBAMFile) ... ok testOpt (SamFile_test.BasicTestBAMFile) ... ok testPairedBools (SamFile_test.BasicTestBAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestBAMFile) ... ok testTags (SamFile_test.BasicTestBAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestBAMFile) ... ok testARcigar (SamFile_test.BasicTestSAMFetch) ... ok testARcigarstring (SamFile_test.BasicTestSAMFetch) ... ok testARflag (SamFile_test.BasicTestSAMFetch) ... ok testARisize (SamFile_test.BasicTestSAMFetch) ... ok testARmapq (SamFile_test.BasicTestSAMFetch) ... ok testARmpos (SamFile_test.BasicTestSAMFetch) ... ok testARmrnm (SamFile_test.BasicTestSAMFetch) ... ok testARpos (SamFile_test.BasicTestSAMFetch) ... ok testARqname (SamFile_test.BasicTestSAMFetch) ... ok testARqqual (SamFile_test.BasicTestSAMFetch) ... ok testARqual (SamFile_test.BasicTestSAMFetch) ... ok testARquery (SamFile_test.BasicTestSAMFetch) ... ok testARrname (SamFile_test.BasicTestSAMFetch) ... ok testARseq (SamFile_test.BasicTestSAMFetch) ... ok testAddTags (SamFile_test.BasicTestSAMFetch) ... ok testAddTagsType (SamFile_test.BasicTestSAMFetch) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFetch) ... ok testMissingOpt (SamFile_test.BasicTestSAMFetch) ... ok testOpt (SamFile_test.BasicTestSAMFetch) ... ok testPairedBools (SamFile_test.BasicTestSAMFetch) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFetch) ... ok testTags (SamFile_test.BasicTestSAMFetch) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFetch) ... ok testARcigar (SamFile_test.BasicTestSAMFile) ... ok testARcigarstring (SamFile_test.BasicTestSAMFile) ... ok testARflag (SamFile_test.BasicTestSAMFile) ... ok testARisize (SamFile_test.BasicTestSAMFile) ... ok testARmapq (SamFile_test.BasicTestSAMFile) ... ok testARmpos (SamFile_test.BasicTestSAMFile) ... ok testARmrnm (SamFile_test.BasicTestSAMFile) ... ok testARpos (SamFile_test.BasicTestSAMFile) ... ok testARqname (SamFile_test.BasicTestSAMFile) ... ok testARqqual (SamFile_test.BasicTestSAMFile) ... ok testARqual (SamFile_test.BasicTestSAMFile) ... ok testARquery (SamFile_test.BasicTestSAMFile) ... ok testARrname (SamFile_test.BasicTestSAMFile) ... ok testARseq (SamFile_test.BasicTestSAMFile) ... ok testAddTags (SamFile_test.BasicTestSAMFile) ... ok testAddTagsType (SamFile_test.BasicTestSAMFile) ... ok testEmptyOpt (SamFile_test.BasicTestSAMFile) ... ok testMissingOpt (SamFile_test.BasicTestSAMFile) ... ok testOpt (SamFile_test.BasicTestSAMFile) ... ok testPairedBools (SamFile_test.BasicTestSAMFile) ... ok testPresentOptionalFields (SamFile_test.BasicTestSAMFile) ... ok testTags (SamFile_test.BasicTestSAMFile) ... ok testTagsUpdatingFloat (SamFile_test.BasicTestSAMFile) ... ok testBlocks (SamFile_test.TestAlignedRead) ... ok testEmpty (SamFile_test.TestAlignedRead) ... ok build an example read. ... ok testPositions (SamFile_test.TestAlignedRead) ... ok testStrOfEmptyRead (SamFile_test.TestAlignedRead) ... ok test for tag parsing ... ok check if updating fields affects other variable length data ... ok issue 135: inplace update of sequence and quality score. ... ok check if updating tlen works ... ok testReadTags (SamFile_test.TestBTagBam) ... ok testReadWriteTags (SamFile_test.TestBTagBam) ... ok testReadTags (SamFile_test.TestBTagSam) ... ok testReadWriteTags (SamFile_test.TestBTagSam) ... ok testClipping (SamFile_test.TestClipping) ... ok testManager (SamFile_test.TestContextManager) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstruction) ... ok check if individual reads are binary equal. ... ok testBAMWholeFile (SamFile_test.TestDeNovoConstructionUserTags) ... ok testDoubleFetch (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchUntilEOF (SamFile_test.TestDoubleFetch) ... ok testDoubleFetchWithRegion (SamFile_test.TestDoubleFetch) ... ok testEmptyHeader (SamFile_test.TestEmptyHeader) ... ok testBackwardsOrderNewFormat (SamFile_test.TestExceptions) ... ok testBackwardsOrderOldFormat (SamFile_test.TestExceptions) ... ok testBadContig (SamFile_test.TestExceptions) ... ok testMeaninglessCrap (SamFile_test.TestExceptions) ... ok testMissingFile (SamFile_test.TestExceptions) ... ok testOutOfRangNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeLargeOldFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeNewFormat (SamFile_test.TestExceptions) ... ok testOutOfRangeNegativeOldFormat (SamFile_test.TestExceptions) ... ok see issue 44 ... ok a float tag before another exposed a parsing bug in bam_aux_get. ... ok testRead (SamFile_test.TestHeader1000Genomes) ... ok testHeaders (SamFile_test.TestHeaderBam) ... ok testNameMapping (SamFile_test.TestHeaderBam) ... ok testHeaders (SamFile_test.TestHeaderSam) ... ok testNameMapping (SamFile_test.TestHeaderSam) ... ok test if autodetection works. ... ok see issue 116 ... ok see issue 117 ... ok test that access to a closed samfile raises ValueError. ... ok testFetchFromClosedFile (SamFile_test.TestIO) ... ok test IteratorRowHead ... ok see issue 104. ... ok testReadSamWithoutHeader (SamFile_test.TestIO) ... ok see issue 104. ... ok testReadWriteBam (SamFile_test.TestIO) ... ok testReadWriteSamWithHeader (SamFile_test.TestIO) ... ok testReadWriteSamWithoutHeader (SamFile_test.TestIO) ... ok read from bam file without index. ... ok test the inverse, is point-wise pileup accurate. ... ok check random access per contig ... ok check random access per contig ... ok check random access per range ... ok check random access per range ... ok see issue 131 ... ok testStart (SamFile_test.TestIteratorColumn2) ... ok see issue 107. ... ok check random access per contig ... ok check random access per range ... ok compare results from iterator with those from samtools. ... ok when creating a read with a large entry in the tag field ... ok testBAM (SamFile_test.TestLargeOptValues) ... ok testSAM (SamFile_test.TestLargeOptValues) ... ok testFail1 (SamFile_test.TestLogging) ... ok testNoFail1 (SamFile_test.TestLogging) ... ok testNoFail2 (SamFile_test.TestLogging) ... ok testAllStepper (SamFile_test.TestPileup) ... ok testSamtoolsStepper (SamFile_test.TestPileup) ... ok test if exception is raised if pileup col is accessed after ... ok testPileupColumn (SamFile_test.TestPileupObjects) ... ok testPileupRead (SamFile_test.TestPileupObjects) ... ok testFTPFetch (SamFile_test.TestRemoteFileFTP) ... ok testFTPView (SamFile_test.TestRemoteFileFTP) ... ok testFetch (SamFile_test.TestRemoteFileHTTP) ... ok testFetchAll (SamFile_test.TestRemoteFileHTTP) ... ok testView (SamFile_test.TestRemoteFileHTTP) ... ok testIndex (SamFile_test.TestSamfileIndex) ... ok testCount (SamFile_test.TestSamfileUtilityFunctions) ... ok test if total number of mapped/unmapped reads is correct. ... ok test mate access. ... ok testIndex (SamFile_test.TestSamtoolsProxy) ... ok testSort (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testView (SamFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file' ok testCigar (SamFile_test.TestTagParsing) ... ok testCigarString (SamFile_test.TestTagParsing) ... ok see issue 115 ... ok testNegativeIntegers (SamFile_test.TestTagParsing) ... ok testNegativeIntegers2 (SamFile_test.TestTagParsing) ... ok testBAM (SamFile_test.TestUnmappedReads) ... ok testOpenBamAsSam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsBam (SamFile_test.TestWrongFormat) ... ok testOpenFastaAsSam (SamFile_test.TestWrongFormat) ... ok testOpenSamAsBam (SamFile_test.TestWrongFormat) ... ok test_samtools_processing (StreamFiledescriptors_test.StreamTest) ... ok test_text_processing (StreamFiledescriptors_test.StreamTest) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok testBase (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok testBase (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionFromCopy (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithLines (VariantFile_test.TestConstructionVCFWithContigs) ... ok testConstructionWithRecords (VariantFile_test.TestConstructionVCFWithContigs) ... ok testIterator (VariantFile_test.TestHeader) ... ok testStr (VariantFile_test.TestHeader) ... ok testOpen (VariantFile_test.TestIndexFilename) ... ok testVCF (VariantFile_test.TestMissingGenotypes) ... ok testVCFGZ (VariantFile_test.TestMissingGenotypes) ... ok testDetectBCF (VariantFile_test.TestOpening) ... ok testDetectVCF (VariantFile_test.TestOpening) ... [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.) ok testDetectVCFGZ (VariantFile_test.TestOpening) ... ok testEmptyFileVCF (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZOnlyHeader (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFGZWithoutIndex (VariantFile_test.TestOpening) ... ok testEmptyFileVCFOnlyHeader (VariantFile_test.TestOpening) ... ok testMissingFile (VariantFile_test.TestOpening) ... ok testMissingFileVCFGZ (VariantFile_test.TestOpening) ... ok testAlleles (VariantFile_test.TestParsing) ... ok testAlt (VariantFile_test.TestParsing) ... ok testChrom (VariantFile_test.TestParsing) ... ok testFilter (VariantFile_test.TestParsing) ... ok testFormat (VariantFile_test.TestParsing) ... ok testId (VariantFile_test.TestParsing) ... ok testInfo (VariantFile_test.TestParsing) ... ok testPos (VariantFile_test.TestParsing) ... ok testQual (VariantFile_test.TestParsing) ... ok testRef (VariantFile_test.TestParsing) ... ok testSampleAlleleIndices (VariantFile_test.TestParsing) ... ok testSampleAlleles (VariantFile_test.TestParsing) ... ok testSampleFormats (VariantFile_test.TestParsing) ... ok testStart (VariantFile_test.TestParsing) ... ok testStop (VariantFile_test.TestParsing) ... ok testBase (VariantFile_test.TestSettingRecordValues) ... ok testGenotype (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSetQual (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) ok testSubsetting (VariantFile_test.TestSubsetting) ... In file included from /<>/python-pysam-0.10.0+ds/tests/_compile_test.c:439:0: /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int hts_get_verbosity(); ^~~ ok testCount (compile_test.BAMTest) ... ok testCount (compile_test.GTFTest) ... ok testFetch (faidx_test.TestFastaFile) ... ok testFetchErrors (faidx_test.TestFastaFile) ... ok testLength (faidx_test.TestFastaFile) ... ok test out of range access. ... ok testSequenceLengths (faidx_test.TestFastaFile) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndex) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndex) ... ok testGarbageIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testOpenWithoutIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok testCounts (faidx_test.TestFastqFileFastq) ... ok testManager (faidx_test.TestFastqFileFastq) ... ok testMissingFile (faidx_test.TestFastqFileFastq) ... ok testSequence (faidx_test.TestFastqFileFastq) ... ok testCounts (faidx_test.TestFastxFileFasta) ... ok testManager (faidx_test.TestFastxFileFasta) ... ok testMissingFile (faidx_test.TestFastxFileFasta) ... ok testSequence (faidx_test.TestFastxFileFasta) ... ok testCounts (faidx_test.TestFastxFileFastq) ... ok testManager (faidx_test.TestFastxFileFastq) ... ok testMissingFile (faidx_test.TestFastxFileFastq) ... ok testSequence (faidx_test.TestFastxFileFastq) ... ok testCounts (faidx_test.TestFastxFileFastqStream) ... ok testManager (faidx_test.TestFastxFileFastqStream) ... ok testMissingFile (faidx_test.TestFastxFileFastqStream) ... ok testSequence (faidx_test.TestFastxFileFastqStream) ... ok testIteration (faidx_test.TestFastxFileWithEmptySequence) ... ok testStatements (samtools_test.BcftoolsTest) ... [W::bcf_hdr_check_sanity] GL should be declared as Number=G ok testEmptyIndex (samtools_test.EmptyIndexTest) ... ok testStatements (samtools_test.PysamTest) ... ok testStatements (samtools_test.SamtoolsTest) ... ok testDoubleCalling (samtools_test.StdoutTest) ... ok testSaveStdout (samtools_test.StdoutTest) ... ok testWithRedirectedStdout (samtools_test.StdoutTest) ... ok testWithoutRedirectedStdout (samtools_test.StdoutTest) ... ok testReturnValueData (samtools_test.TestReturnType) ... ok testReturnValueString (samtools_test.TestReturnType) ... ok testBED (tabix_test.TestBackwardsCompatibility) ... ok testBED0v23 (tabix_test.TestBackwardsCompatibility) ... ok testBED0v26 (tabix_test.TestBackwardsCompatibility) ... ok testEmpty (tabix_test.TestBackwardsCompatibility) ... ok testVCF (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v23 (tabix_test.TestBackwardsCompatibility) ... ok testVCF0v26 (tabix_test.TestBackwardsCompatibility) ... ok testRead (tabix_test.TestBed) ... ok testWrite (tabix_test.TestBed) ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok see also issue 106 ... ok test indexing via preset. ... ok test indexing via preset. ... ok testManager (tabix_test.TestContextManager) ... ok testCopy (tabix_test.TestGTF) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestGTF) ... ok testSetting (tabix_test.TestGTF) ... ok testUnset (tabix_test.TestGTF) ... ok testWrite (tabix_test.TestGTF) ... ok testAll (tabix_test.TestGZFile) ... ok testFetchAll (tabix_test.TestIndexArgument) ... ok test indexing via preset. ... ok testGTFTooFewFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testGTFTooManyFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok testAll (tabix_test.TestIterationWithComments) ... ok testGetContigs (tabix_test.TestIterationWithComments) ... ok testHeader (tabix_test.TestIterationWithComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithComments) ... ok testPerContig (tabix_test.TestIterationWithComments) ... ok testPerContig2 (tabix_test.TestIterationWithComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithComments) ... ok testPerInterval (tabix_test.TestIterationWithComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok testAll (tabix_test.TestIterationWithoutComments) ... ok testGetContigs (tabix_test.TestIterationWithoutComments) ... ok testHeader (tabix_test.TestIterationWithoutComments) ... ok testInvalidIntervals (tabix_test.TestIterationWithoutComments) ... ok testPerContig (tabix_test.TestIterationWithoutComments) ... ok testPerContig2 (tabix_test.TestIterationWithoutComments) ... ok testPerContigFromStart (tabix_test.TestIterationWithoutComments) ... ok testPerContigToEnd (tabix_test.TestIterationWithoutComments) ... ok testPerInterval (tabix_test.TestIterationWithoutComments) ... ok test if access with various region strings ... ok test repeated opening of the same file. ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIterators) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileCompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsFileUncompressed) ... ok test for error when iterating from closed file. ... ok test for error when iterating from file that has been closed ... ok testIteration (tabix_test.TestIteratorsGenericCompressed) ... ok testDisjointIterators (tabix_test.TestMultipleIterators) ... ok testDoubleFetch (tabix_test.TestMultipleIterators) ... ok testJoinedIterators (tabix_test.TestMultipleIterators) ... ok testScope (tabix_test.TestMultipleIterators) ... ok testCopy (tabix_test.TestParser) ... ok test iteration from compressed file. ... ok test iteration from uncompressed file. ... ok testRead (tabix_test.TestParser) ... ok testUnset (tabix_test.TestParser) ... ok testWrite (tabix_test.TestParser) ... ok testFetchAll (tabix_test.TestRemoteFileHTTP) ... ok testHeader (tabix_test.TestRemoteFileHTTP) ... ok testFromTabix (tabix_test.TestUnicode) ... ok testFromVCF (tabix_test.TestUnicode) ... ok testRead (tabix_test.TestVCFFromTabix) ... ok testWrite (tabix_test.TestVCFFromTabix) ... ok testConnecting (tabix_test.TestVCFFromVCF) ... ok testParsing (tabix_test.TestVCFFromVCF) ... ok testConnecting (tabix_test.TestVCFFromVariantFile) ... ok testParsing (tabix_test.TestVCFFromVariantFile) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_10) ... ok testParsing (tabix_test.TestVCFFromVariantFile_10) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_11) ... ok testParsing (tabix_test.TestVCFFromVariantFile_11) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_12) ... ok testParsing (tabix_test.TestVCFFromVariantFile_12) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_13) ... ok testParsing (tabix_test.TestVCFFromVariantFile_13) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_15) ... ok testParsing (tabix_test.TestVCFFromVariantFile_15) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_16) ... ok testParsing (tabix_test.TestVCFFromVariantFile_16) ... [W::bcf_hdr_check_sanity] PL should be declared as Number=G [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_18) ... ok testParsing (tabix_test.TestVCFFromVariantFile_18) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_2) ... ok testParsing (tabix_test.TestVCFFromVariantFile_2) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_20) ... ok testParsing (tabix_test.TestVCFFromVariantFile_20) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_21) ... ok testParsing (tabix_test.TestVCFFromVariantFile_21) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_22) ... ok testParsing (tabix_test.TestVCFFromVariantFile_22) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_23) ... ok testParsing (tabix_test.TestVCFFromVariantFile_23) ... [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String ok testConnecting (tabix_test.TestVCFFromVariantFile_24) ... ok testParsing (tabix_test.TestVCFFromVariantFile_24) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_3) ... ok testParsing (tabix_test.TestVCFFromVariantFile_3) ... [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_4) ... ok testParsing (tabix_test.TestVCFFromVariantFile_4) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_5) ... ok testParsing (tabix_test.TestVCFFromVariantFile_5) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) ok testConnecting (tabix_test.TestVCFFromVariantFile_6) ... ok testParsing (tabix_test.TestVCFFromVariantFile_6) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_7) ... ok testParsing (tabix_test.TestVCFFromVariantFile_7) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_8) ... ok testParsing (tabix_test.TestVCFFromVariantFile_8) ... [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 ok testConnecting (tabix_test.TestVCFFromVariantFile_9) ... ok testParsing (tabix_test.TestVCFFromVariantFile_9) ... [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.) ok testConnecting (tabix_test.TestVCFFromVariantFile_issue85) ... ok testParsing (tabix_test.TestVCFFromVariantFile_issue85) ... ok testConnecting (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testParsing (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok testRead (tabix_test.VCFFromTabixTest_10) ... ok testWrite (tabix_test.VCFFromTabixTest_10) ... ok testRead (tabix_test.VCFFromTabixTest_11) ... ok testWrite (tabix_test.VCFFromTabixTest_11) ... ok testRead (tabix_test.VCFFromTabixTest_12) ... ok testWrite (tabix_test.VCFFromTabixTest_12) ... ok testRead (tabix_test.VCFFromTabixTest_13) ... ok testWrite (tabix_test.VCFFromTabixTest_13) ... ok testRead (tabix_test.VCFFromTabixTest_15) ... ok testWrite (tabix_test.VCFFromTabixTest_15) ... ok testRead (tabix_test.VCFFromTabixTest_16) ... ok testWrite (tabix_test.VCFFromTabixTest_16) ... ok testRead (tabix_test.VCFFromTabixTest_18) ... ok testWrite (tabix_test.VCFFromTabixTest_18) ... ok testRead (tabix_test.VCFFromTabixTest_2) ... ok testWrite (tabix_test.VCFFromTabixTest_2) ... ok testRead (tabix_test.VCFFromTabixTest_20) ... ok testWrite (tabix_test.VCFFromTabixTest_20) ... ok testRead (tabix_test.VCFFromTabixTest_21) ... ok testWrite (tabix_test.VCFFromTabixTest_21) ... ok testRead (tabix_test.VCFFromTabixTest_22) ... ok testWrite (tabix_test.VCFFromTabixTest_22) ... ok testRead (tabix_test.VCFFromTabixTest_23) ... ok testWrite (tabix_test.VCFFromTabixTest_23) ... ok testRead (tabix_test.VCFFromTabixTest_24) ... ok testWrite (tabix_test.VCFFromTabixTest_24) ... ok testRead (tabix_test.VCFFromTabixTest_3) ... ok testWrite (tabix_test.VCFFromTabixTest_3) ... ok testRead (tabix_test.VCFFromTabixTest_4) ... ok testWrite (tabix_test.VCFFromTabixTest_4) ... ok testRead (tabix_test.VCFFromTabixTest_5) ... ok testWrite (tabix_test.VCFFromTabixTest_5) ... ok testRead (tabix_test.VCFFromTabixTest_6) ... ok testWrite (tabix_test.VCFFromTabixTest_6) ... ok testRead (tabix_test.VCFFromTabixTest_7) ... ok testWrite (tabix_test.VCFFromTabixTest_7) ... ok testRead (tabix_test.VCFFromTabixTest_8) ... ok testWrite (tabix_test.VCFFromTabixTest_8) ... ok testRead (tabix_test.VCFFromTabixTest_9) ... ok testWrite (tabix_test.VCFFromTabixTest_9) ... ok testRead (tabix_test.VCFFromTabixTest_issue85) ... ok testWrite (tabix_test.VCFFromTabixTest_issue85) ... ok testRead (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testWrite (tabix_test.VCFFromTabixTest_vcf_v42) ... ok testConnecting (tabix_test.VCFFromVCFTest_10) ... ok testParsing (tabix_test.VCFFromVCFTest_10) ... ok testConnecting (tabix_test.VCFFromVCFTest_11) ... ok testParsing (tabix_test.VCFFromVCFTest_11) ... ok testConnecting (tabix_test.VCFFromVCFTest_12) ... ok testParsing (tabix_test.VCFFromVCFTest_12) ... ok testConnecting (tabix_test.VCFFromVCFTest_13) ... ok testParsing (tabix_test.VCFFromVCFTest_13) ... ok testConnecting (tabix_test.VCFFromVCFTest_15) ... ok testParsing (tabix_test.VCFFromVCFTest_15) ... ok testConnecting (tabix_test.VCFFromVCFTest_16) ... ok testParsing (tabix_test.VCFFromVCFTest_16) ... ok testConnecting (tabix_test.VCFFromVCFTest_18) ... ok testParsing (tabix_test.VCFFromVCFTest_18) ... ok testConnecting (tabix_test.VCFFromVCFTest_2) ... ok testParsing (tabix_test.VCFFromVCFTest_2) ... ok testConnecting (tabix_test.VCFFromVCFTest_20) ... ok testParsing (tabix_test.VCFFromVCFTest_20) ... ok testConnecting (tabix_test.VCFFromVCFTest_21) ... ok testParsing (tabix_test.VCFFromVCFTest_21) ... ok testConnecting (tabix_test.VCFFromVCFTest_22) ... ok testParsing (tabix_test.VCFFromVCFTest_22) ... ok testConnecting (tabix_test.VCFFromVCFTest_23) ... ok testParsing (tabix_test.VCFFromVCFTest_23) ... ok testConnecting (tabix_test.VCFFromVCFTest_24) ... ok testParsing (tabix_test.VCFFromVCFTest_24) ... ok testConnecting (tabix_test.VCFFromVCFTest_3) ... ok testParsing (tabix_test.VCFFromVCFTest_3) ... ok testConnecting (tabix_test.VCFFromVCFTest_4) ... ok testParsing (tabix_test.VCFFromVCFTest_4) ... ok testConnecting (tabix_test.VCFFromVCFTest_5) ... ok testParsing (tabix_test.VCFFromVCFTest_5) ... ok testConnecting (tabix_test.VCFFromVCFTest_6) ... ok testParsing (tabix_test.VCFFromVCFTest_6) ... ok testConnecting (tabix_test.VCFFromVCFTest_7) ... ok testParsing (tabix_test.VCFFromVCFTest_7) ... ok testConnecting (tabix_test.VCFFromVCFTest_8) ... ok testParsing (tabix_test.VCFFromVCFTest_8) ... ok testConnecting (tabix_test.VCFFromVCFTest_9) ... ok testParsing (tabix_test.VCFFromVCFTest_9) ... ok testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok test_samtools_python.test_idxstats_parse_split_lines ... ok test_samtools_python.test_bedcov_split_lines ... ok test_samtools_python.test_idxstats_parse ... ok test_samtools_python.test_bedcov ... ok ---------------------------------------------------------------------- Ran 917 tests in 245.124s OK (0, 0) make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py install --root /<>/python-pysam-0.10.0+ds/debian/python-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 -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/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) package init file 'samtools/win32/__init__.py' not found (or not a regular file) running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.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/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.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/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7 creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.pyc -> /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/namedtuple.py to namedtuple.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.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' warning: no files found matching 'pysam/c*.pxd' warning: no files found matching 'pysam/c*.pyx' warning: no files found matching 'pysam/c*.c' 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 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/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.10.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:184: /usr/bin/python3.6 setup.py install --root /<>/python-pysam-0.10.0+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 -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/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) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/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/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.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/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.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/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6 creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbgzf.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.cpython-36m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/__init__.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/version.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/Pileup.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/bcftools.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/samtools.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/config.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/__pycache__/utils.cpython-36.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/samtools.py to samtools.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/version.py to version.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/utils.py to utils.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/__init__.py to __init__.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/Pileup.py to Pileup.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/namedtuple.py to namedtuple.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__init__.py to __init__.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/config.py to config.cpython-36.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/bcftools.py to bcftools.cpython-36.pyc running install_egg_info running 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 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' warning: no files found matching 'pysam/c*.pxd' warning: no files found matching 'pysam/c*.pyx' warning: no files found matching 'pysam/c*.c' 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 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/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam-0.10.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:184: /usr/bin/python3 setup.py install --root /<>/python-pysam-0.10.0+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 -> /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/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) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/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/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.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/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.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/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5 creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbgzf.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samfile_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/tabix_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/pysam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/kprobaln.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/errmod.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_tview.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_stream.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/htslib_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_util.h -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam creating /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/samtools.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/__init__.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/Pileup.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/config.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/utils.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/bcftools.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__pycache__/version.cpython-35.pyc -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.pxd -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam copying /<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.cpython-35m-aarch64-linux-gnu.so -> /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/samtools.py to samtools.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/version.py to version.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/utils.py to utils.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/__init__.py to __init__.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/Pileup.py to Pileup.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/namedtuple.py to namedtuple.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__init__.py to __init__.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/config.py to config.cpython-35.pyc byte-compiling /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/bcftools.py to bcftools.cpython-35.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.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' warning: no files found matching 'pysam/c*.pxd' warning: no files found matching 'pysam/c*.pyx' warning: no files found matching 'pysam/c*.c' 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 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/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'tests/pysam_data' warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.10.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam-0.10.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>/python-pysam-0.10.0+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ *.fq.gz make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/python-pysam-0.10.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "*.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 dh_install -Xtest.gtf.gz make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:322: renaming libcalignedsegment.so to libcalignedsegment.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcalignmentfile.so to libcalignmentfile.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcbcf.so to libcbcf.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcbgzf.so to libcbgzf.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcfaidx.so to libcfaidx.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libchtslib.so to libchtslib.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcsamfile.so to libcsamfile.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libctabix.so to libctabix.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libctabixproxies.so to libctabixproxies.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcutils.so to libcutils.aarch64-linux-gnu.so I: dh_python2 fs:322: renaming libcvcf.so to libcvcf.aarch64-linux-gnu.so dh_python3 -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python-pysam-dbgsym (in debian/.debhelper/python-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python-pysam/dbgsym-root/DEBIAN/control, package python-pysam-dbgsym, directory debian/.debhelper/python-pysam/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pysam/python-pysam-dbgsym_0.10.0+ds-2build1_arm64.deb'. Renaming python-pysam-dbgsym_0.10.0+ds-2build1_arm64.deb to python-pysam-dbgsym_0.10.0+ds-2build1_arm64.ddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python-pysam (in debian/python-pysam); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python-pysam/DEBIAN/control, package python-pysam, directory debian/python-pysam pkgstripfiles: Truncating usr/share/doc/python-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam' in '../python-pysam_0.10.0+ds-2build1_arm64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python3-pysam/dbgsym-root/DEBIAN/control, package python3-pysam-dbgsym, directory debian/.debhelper/python3-pysam/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.10.0+ds-2build1_arm64.deb'. Renaming python3-pysam-dbgsym_0.10.0+ds-2build1_arm64.deb to python3-pysam-dbgsym_0.10.0+ds-2build1_arm64.ddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: Truncating usr/share/doc/python3-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.10.0+ds-2build1_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-pysam_0.10.0+ds-2build1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build python-pysam-0.10.0+ds dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170514-1507 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.10.0+ds-2build1_arm64.changes: --------------------------------------------- Format: 1.8 Date: Sun, 14 May 2017 20:02:02 +0530 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: arm64 Version: 0.10.0+ds-2build1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Bhavani Shankar Description: python-pysam - interface for the SAM/BAM sequence alignment and mapping format ( python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Changes: python-pysam (0.10.0+ds-2build1) artful; urgency=medium . * Rebuild for python 3.6 support. 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It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 2. drwxr-xr-x root/root 0 2017-05-14 14:32 ./ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/lib/ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info/ -rw-r--r-- root/root 1146 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info/not-zip-safe -rw-r--r-- root/root 6 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam-0.10.0.egg-info/top_level.txt drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam/ -rw-r--r-- root/root 8305 2017-01-22 19:32 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./usr/lib/python2.7/dist-packages/pysam/include/bcftools/rbuf.h -rw-r--r-- root/root 2621 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/tsv2vcf.h -rw-r--r-- root/root 2387 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/vcmp.h -rw-r--r-- root/root 33 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/version.h drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/ -rw-r--r-- root/root 20987 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam.h -rw-r--r-- root/root 5126 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam2bcf.h -rw-r--r-- root/root 2273 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam_endian.h -rw-r--r-- root/root 2058 2017-01-22 19:32 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam_lpileup.h -rw-r--r-- root/root 1842 2017-01-22 19:32 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2017-05-14 14:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/share/doc/python-pysam/ -rw-r--r-- root/root 1885 2017-05-14 14:32 ./usr/share/doc/python-pysam/changelog.Debian.gz -rw-r--r-- root/root 6835 2017-05-04 13:06 ./usr/share/doc/python-pysam/copyright drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-05-14 14:32 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 211 2017-05-04 13:06 ./usr/share/lintian/overrides/python-pysam python3-pysam_0.10.0+ds-2build1_arm64.deb ----------------------------------------- new debian package, version 2.0. size 1389748 bytes: control archive=3523 bytes. 788 bytes, 17 lines control 8582 bytes, 88 lines md5sums 172 bytes, 9 lines * postinst #!/bin/sh 401 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.10.0+ds-2build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7636 Depends: libc6 (>= 2.17), libhts1 (>= 1.3), zlib1g (>= 1:1.1.4), python3 (<< 3.7), python3 (>= 3.5~), python3:any (>= 3.3.2-2~) Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . 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./usr/share/lintian/overrides/ -rw-r--r-- root/root 209 2017-05-04 13:06 ./usr/share/lintian/overrides/python3-pysam +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 234256 Build-Time: 1909 Distribution: artful-proposed Host Architecture: arm64 Install-Time: 51 Job: python-pysam_0.10.0+ds-2build1.dsc Machine Architecture: arm64 Package: python-pysam Package-Time: 1962 Source-Version: 0.10.0+ds-2build1 Space: 234256 Status: successful Version: 0.10.0+ds-2build1 -------------------------------------------------------------------------------- Finished at 20170514-1507 Build needed 00:32:42, 234256k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12582255'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12582255/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12582255'] Unmounting chroot for build PACKAGEBUILD-12582255... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12582255'] Removing build PACKAGEBUILD-12582255