https://launchpad.net/ubuntu/+source/python-pysam/0.15.1+ds-1/+build/15634522 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-024 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:15:48 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.5 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 10 Nov 01:46:41 ntpdate[1838]: adjust time server 10.211.37.1 offset 0.078473 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15634522 /home/buildd/filecache-default/bf137a8dadabbe066906202a7cb9d7a8e3a99968 Creating target for build PACKAGEBUILD-15634522 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15634522 Starting target for build PACKAGEBUILD-15634522 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15634522 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15634522 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15634522 Updating target for build PACKAGEBUILD-15634522 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 Packages [976 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe arm64 Packages [8547 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5084 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 Packages [103 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [64.4 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 Packages [569 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [471 kB] Fetched 16.8 MB in 6s (2830 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: base-files binutils binutils-aarch64-linux-gnu binutils-common cpp cpp-8 dash dmsetup findutils g++ g++-8 gcc gcc-8 gcc-8-base hostname init init-system-helpers libapparmor1 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libgpg-error0 libitm1 libkmod2 liblsan0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 linux-libc-dev lockfile-progs perl perl-base sed systemd systemd-sysv tzdata 54 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 40.0 MB of archives. After this operation, 48.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main arm64 base-files arm64 10.1ubuntu8 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main arm64 dash arm64 0.5.10.2-1 [88.0 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 findutils arm64 4.6.0+git+20181018-1 [290 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main arm64 hostname arm64 3.21 [10.9 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main arm64 libgdbm6 arm64 1.18.1-1 [26.8 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main arm64 libgdbm-compat4 arm64 1.18.1-1 [6016 B] Get:8 http://ftpmaster.internal/ubuntu disco/main arm64 libperl5.28 arm64 5.28.0-3 [3667 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main arm64 perl arm64 5.28.0-3 [204 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main arm64 perl-base arm64 5.28.0-3 [1398 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.2 [616 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 sed arm64 4.5-2 [182 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 init-system-helpers all 1.55 [38.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 systemd-sysv arm64 239-7ubuntu10.1 [9404 B] Get:15 http://ftpmaster.internal/ubuntu disco/main arm64 libapparmor1 arm64 2.12-4ubuntu10 [29.1 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main arm64 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:17 http://ftpmaster.internal/ubuntu disco/main arm64 libcap-ng0 arm64 0.7.9-1build1 [10.5 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main arm64 libaudit1 arm64 1:2.8.3-1ubuntu3 [38.1 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libgpg-error0 arm64 1.32-3 [53.4 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libkmod2 arm64 25-1ubuntu1.1 [38.7 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 systemd arm64 239-7ubuntu10.1 [2757 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libsystemd0 arm64 239-7ubuntu10.1 [195 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 init arm64 1.55 [6476 B] Get:24 http://ftpmaster.internal/ubuntu disco/main arm64 libcc1-0 arm64 8.2.0-9ubuntu1 [36.3 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main arm64 libgomp1 arm64 8.2.0-9ubuntu1 [69.6 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main arm64 libitm1 arm64 8.2.0-9ubuntu1 [24.4 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main arm64 libatomic1 arm64 8.2.0-9ubuntu1 [9124 B] Get:28 http://ftpmaster.internal/ubuntu disco/main arm64 libasan5 arm64 8.2.0-9ubuntu1 [336 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main arm64 liblsan0 arm64 8.2.0-9ubuntu1 [121 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main arm64 libtsan0 arm64 8.2.0-9ubuntu1 [269 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main arm64 libubsan1 arm64 8.2.0-9ubuntu1 [113 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main arm64 gcc-8-base arm64 8.2.0-9ubuntu1 [18.6 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main arm64 libstdc++6 arm64 8.2.0-9ubuntu1 [372 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main arm64 g++-8 arm64 8.2.0-9ubuntu1 [6548 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main arm64 libstdc++-8-dev arm64 8.2.0-9ubuntu1 [1513 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main arm64 libgcc-8-dev arm64 8.2.0-9ubuntu1 [857 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main arm64 gcc-8 arm64 8.2.0-9ubuntu1 [6470 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main arm64 cpp-8 arm64 8.2.0-9ubuntu1 [5713 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main arm64 libgcc1 arm64 1:8.2.0-9ubuntu1 [34.3 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main arm64 libbinutils arm64 2.31.1-7ubuntu1 [462 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main arm64 binutils-common arm64 2.31.1-7ubuntu1 [194 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main arm64 binutils arm64 2.31.1-7ubuntu1 [3364 B] Get:43 http://ftpmaster.internal/ubuntu disco/main arm64 binutils-aarch64-linux-gnu arm64 2.31.1-7ubuntu1 [2173 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main arm64 libselinux1 arm64 2.8-1build2 [64.9 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main arm64 libsemanage-common all 2.8-1build2 [6892 B] Get:46 http://ftpmaster.internal/ubuntu disco/main arm64 libsemanage1 arm64 2.8-1build2 [79.7 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libudev1 arm64 239-7ubuntu10.1 [50.1 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libseccomp2 arm64 2.3.3-3ubuntu2 [38.6 kB] Get:49 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libdevmapper1.02.1 arm64 2:1.02.145-4.1ubuntu4 [109 kB] Get:50 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 dmsetup arm64 2:1.02.145-4.1ubuntu4 [67.6 kB] Get:51 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libsqlite3-0 arm64 3.25.3-1 [490 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main arm64 tzdata all 2018g-1 [188 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main arm64 g++ arm64 4:8.2.0-2ubuntu2 [1592 B] Get:54 http://ftpmaster.internal/ubuntu disco/main arm64 gcc arm64 4:8.2.0-2ubuntu2 [5232 B] Get:55 http://ftpmaster.internal/ubuntu disco/main arm64 cpp arm64 4:8.2.0-2ubuntu2 [27.6 kB] Get:56 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 linux-libc-dev arm64 4.18.0-11.12 [1019 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main arm64 lockfile-progs arm64 0.1.18 [9748 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.0 MB in 1s (32.3 MB/s) (Reading database ... 12627 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_arm64.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12627 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-1_arm64.deb ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... Setting up dash (0.5.10.2-1) ... 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Setting up liblsan0:arm64 (8.2.0-9ubuntu1) ... Setting up libgdbm6:arm64 (1.18.1-1) ... Setting up binutils-common:arm64 (2.31.1-7ubuntu1) ... Setting up perl-modules-5.28 (5.28.0-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libsqlite3-0:arm64 (3.25.3-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:arm64 (1.18.1-1) ... Setting up lockfile-progs (0.1.18) ... Setting up libasan5:arm64 (8.2.0-9ubuntu1) ... Setting up libitm1:arm64 (8.2.0-9ubuntu1) ... Setting up libubsan1:arm64 (8.2.0-9ubuntu1) ... Setting up libbinutils:arm64 (2.31.1-7ubuntu1) ... Setting up libperl5.28:arm64 (5.28.0-3) ... Setting up perl (5.28.0-3) ... Setting up binutils-aarch64-linux-gnu (2.31.1-7ubuntu1) ... Setting up libgcc-8-dev:arm64 (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:arm64 (8.2.0-9ubuntu1) ... Setting up gcc-8 (8.2.0-9ubuntu1) ... Setting up g++-8 (8.2.0-9ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15634522 arm64 disco-proposed -c chroot:build-PACKAGEBUILD-15634522 --arch=arm64 --dist=disco-proposed --nolog python-pysam_0.15.1+ds-1.dsc Initiating build PACKAGEBUILD-15634522 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:15:48 UTC 2018 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-024.buildd +==============================================================================+ | python-pysam 0.15.1+ds-1 (arm64) 10 Nov 2018 01:47 | +==============================================================================+ Package: python-pysam Version: 0.15.1+ds-1 Source Version: 0.15.1+ds-1 Distribution: disco-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/python-pysam-CLsI1a/python-pysam-0.15.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-CLsI1a' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15634522/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.15.1+ds-1.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-wLBakZ/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-wLBakZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-wLBakZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-wLBakZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-wLBakZ/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-wLBakZ/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (150 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 packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-wLBakZ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14518 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 (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest Filtered Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<>/resolver-4_NgbG/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'. Ign:1 copy:/<>/resolver-4_NgbG/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4_NgbG/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4_NgbG/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4_NgbG/apt_archive ./ Sources [315 B] Get:5 copy:/<>/resolver-4_NgbG/apt_archive ./ Packages [622 B] Fetched 3056 B in 0s (145 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 packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtool libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-atomicwrites python-attr python-dev python-funcsigs python-minimal python-more-itertools python-pkg-resources python-pluggy python-py python-pytest python-setuptools python-six python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-lib2to3 python3-minimal python3-more-itertools python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3-six python3.7 python3.7-dev python3.7-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 krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python-attr-doc python-funcsigs-doc subversion python-pytest-xdist python-mock python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.7-venv python3.7-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtool libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-atomicwrites python-attr python-dev python-funcsigs python-minimal python-more-itertools python-pkg-resources python-pluggy python-py python-pytest python-setuptools python-six python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-lib2to3 python3-minimal python3-more-itertools python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3-six python3.7 python3.7-dev python3.7-minimal samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev 0 upgraded, 124 newly installed, 0 to remove and 0 not upgraded. Need to get 70.7 MB of archives. After this operation, 226 MB of additional disk space will be used. Get:1 copy:/<>/resolver-4_NgbG/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [952 B] Get:2 http://ftpmaster.internal/ubuntu disco/main arm64 libpython3.7-minimal arm64 3.7.1-1 [543 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main arm64 libexpat1 arm64 2.2.6-1 [68.2 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main arm64 python3.7-minimal arm64 3.7.1-1 [1358 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main arm64 python3-minimal arm64 3.7.1-1ubuntu1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main arm64 mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main arm64 libmpdec2 arm64 2.4.2-2 [74.0 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main arm64 libpython3.7-stdlib arm64 3.7.1-1 [1637 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main arm64 python3.7 arm64 3.7.1-1 [272 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main arm64 libpython3-stdlib arm64 3.7.1-1ubuntu1 [7128 B] Get:11 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libsigsegv2 arm64 2.12-2 [13.3 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main arm64 m4 arm64 1.4.18-1ubuntu1 [194 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main arm64 autoconf all 2.69-11 [322 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:45 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 automake all 1:1.16.1-4 [522 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main arm64 autopoint all 0.19.8.1-8 [412 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main arm64 libroken18-heimdal arm64 7.5.0+dfsg-2 [35.4 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main arm64 libasn1-8-heimdal arm64 7.5.0+dfsg-2 [130 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main arm64 libheimbase1-heimdal arm64 7.5.0+dfsg-2 [24.9 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main arm64 libhcrypto4-heimdal arm64 7.5.0+dfsg-2 [75.2 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main arm64 libwind0-heimdal arm64 7.5.0+dfsg-2 [46.9 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main arm64 libhx509-5-heimdal arm64 7.5.0+dfsg-2 [88.5 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main arm64 libkrb5-26-heimdal arm64 7.5.0+dfsg-2 [170 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main arm64 libheimntlm0-heimdal arm64 7.5.0+dfsg-2 [13.4 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main arm64 libgssapi3-heimdal arm64 7.5.0+dfsg-2 [79.3 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main arm64 libsasl2-modules-db arm64 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.4 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main arm64 libsasl2-2 arm64 2.1.27~101-g0780600+dfsg-3ubuntu2 [43.1 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main arm64 libldap-common all 2.4.46+dfsg-5ubuntu2 [16.6 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main arm64 libldap-2.4-2 arm64 2.4.46+dfsg-5ubuntu2 [145 kB] Get:60 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libnghttp2-14 arm64 1.34.0-1 [75.9 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [49.8 kB] Get:62 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libcurl3-gnutls arm64 7.61.0-1ubuntu2.2 [198 kB] Get:63 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 libhts2 arm64 1.9-3 [277 kB] Get:64 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 bcftools arm64 1.9-1 [477 kB] Get:65 http://ftpmaster.internal/ubuntu disco/universe arm64 cython arm64 0.28.4-1build1 [1820 kB] Get:66 http://ftpmaster.internal/ubuntu disco/universe arm64 cython3 arm64 0.28.4-1build1 [1856 kB] Get:67 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libtool all 2.4.6-6 [195 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main arm64 dh-autoreconf all 19 [16.1 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main arm64 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:70 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 libfile-stripnondeterminism-perl all 0.044-1 [15.0 kB] Get:71 http://ftpmaster.internal/ubuntu disco-proposed/main arm64 dh-strip-nondeterminism all 0.044-1 [5124 B] Get:72 http://ftpmaster.internal/ubuntu disco/main arm64 dwz arm64 0.12-2 [68.1 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main arm64 libcroco3 arm64 0.6.12-2 [68.2 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main arm64 gettext arm64 0.19.8.1-8 [853 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main arm64 po-debconf all 1.0.20 [232 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main arm64 debhelper all 11.3.2ubuntu1 [883 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main arm64 python3-lib2to3 all 3.7.1-1ubuntu3 [76.5 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main arm64 python3-distutils all 3.7.1-1ubuntu3 [141 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main arm64 dh-python all 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3.7.1-1 [1372 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main arm64 libpython3.7-dev arm64 3.7.1-1 [2374 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main arm64 libpython3-dev arm64 3.7.1-1ubuntu1 [7228 B] Get:93 http://ftpmaster.internal/ubuntu disco/main arm64 libpython3-all-dev arm64 3.7.1-1ubuntu1 [1112 B] Get:94 http://ftpmaster.internal/ubuntu disco/main arm64 python-all arm64 2.7.15-3 [1072 B] Get:95 http://ftpmaster.internal/ubuntu disco/main arm64 python2.7-dev arm64 2.7.15-4ubuntu4 [282 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main arm64 python2-dev arm64 2.7.15-3 [1244 B] Get:97 http://ftpmaster.internal/ubuntu disco/main arm64 python-dev arm64 2.7.15-3 [1216 B] Get:98 http://ftpmaster.internal/ubuntu disco/main arm64 python-all-dev arm64 2.7.15-3 [1096 B] Get:99 http://ftpmaster.internal/ubuntu disco/universe arm64 python-atomicwrites all 1.1.5-2 [6856 B] Get:100 http://ftpmaster.internal/ubuntu disco/main arm64 python-attr all 18.2.0-1 [29.6 kB] 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Get:111 http://ftpmaster.internal/ubuntu disco/main arm64 python3-dev arm64 3.7.1-1ubuntu1 [1308 B] Get:112 http://ftpmaster.internal/ubuntu disco/main arm64 python3-all-dev arm64 3.7.1-1ubuntu1 [1112 B] Get:113 http://ftpmaster.internal/ubuntu disco/universe arm64 python3-atomicwrites all 1.1.5-2 [6932 B] Get:114 http://ftpmaster.internal/ubuntu disco/main arm64 python3-attr all 18.2.0-1 [29.6 kB] Get:115 http://ftpmaster.internal/ubuntu disco/main arm64 python3-six all 1.11.0-2 [11.4 kB] Get:116 http://ftpmaster.internal/ubuntu disco/universe arm64 python3-more-itertools all 4.2.0-1 [39.3 kB] Get:117 http://ftpmaster.internal/ubuntu disco/main arm64 python3-pkg-resources all 40.5.0-1 [99.6 kB] Get:118 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 python3-pluggy all 0.8.0-1 [17.5 kB] Get:119 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 python3-py all 1.7.0-1 [65.5 kB] Get:120 http://ftpmaster.internal/ubuntu disco/universe arm64 python3-pytest all 3.6.4-1 [152 kB] Get:121 http://ftpmaster.internal/ubuntu disco/main arm64 python3-setuptools all 40.5.0-1 [249 kB] Get:122 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 samtools arm64 1.9-1 [401 kB] Get:123 http://ftpmaster.internal/ubuntu disco-proposed/universe arm64 tabix arm64 1.9-3 [309 kB] Get:124 http://ftpmaster.internal/ubuntu disco/main arm64 dh-exec arm64 0.23build1 [23.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.7 MB in 3s (25.7 MB/s) Selecting previously unselected package libpython3.7-minimal:arm64. (Reading database ... 14518 files and directories currently installed.) Preparing to unpack .../libpython3.7-minimal_3.7.1-1_arm64.deb ... Unpacking libpython3.7-minimal:arm64 (3.7.1-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.6-1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.6-1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.1-1_arm64.deb ... Unpacking python3.7-minimal (3.7.1-1) ... Setting up libpython3.7-minimal:arm64 (3.7.1-1) ... Setting up libexpat1:arm64 (2.2.6-1) ... Setting up python3.7-minimal (3.7.1-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 14767 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.1-1ubuntu1_arm64.deb ... Unpacking python3-minimal (3.7.1-1ubuntu1) ... Selecting previously unselected package mime-support. 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Setting up m4 (1.4.18-1ubuntu1) ... Setting up libbsd0:arm64 (0.9.1-1) ... Setting up libkrb5support0:arm64 (1.16-2ubuntu1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7ubuntu2) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:arm64 (1:5.34-2) ... Setting up libcroco3:arm64 (0.6.12-2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:arm64 (7.5.0+dfsg-2) ... Setting up libexpat1-dev:arm64 (2.2.6-1) ... Setting up liblzma-dev:arm64 (5.2.2-1.3) ... Setting up libkeyutils1:arm64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libpython2.7-stdlib:arm64 (2.7.15-4ubuntu4) ... Setting up autopoint (0.19.8.1-8) ... Setting up libmpdec2:arm64 (2.4.2-2) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:arm64 (2.7.15-3) ... Setting up libkrb5-3:arm64 (1.16-2ubuntu1) ... Setting up libpython2.7-dev:arm64 (2.7.15-4ubuntu4) ... Setting up libkrb5-26-heimdal:arm64 (7.5.0+dfsg-2) ... Setting up python2.7-dev (2.7.15-4ubuntu4) ... Setting up libheimntlm0-heimdal:arm64 (7.5.0+dfsg-2) ... Setting up libpython3-dev:arm64 (3.7.1-1ubuntu1) ... Setting up libtool (2.4.6-6) ... Setting up libpython3-stdlib:arm64 (3.7.1-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.7.1-1ubuntu1) ... Setting up python3-six (1.11.0-2) ... Setting up python3-more-itertools (4.2.0-1) ... Setting up python3-pkg-resources (40.5.0-1) ... Setting up python3.7-dev (3.7.1-1) ... Setting up python3-pluggy (0.8.0-1) ... Setting up python2 (2.7.15-3) ... Setting up libgssapi-krb5-2:arm64 (1.16-2ubuntu1) ... Setting up libpython2-dev:arm64 (2.7.15-3) ... Setting up libpython-stdlib:arm64 (2.7.15-3) ... Setting up libpython3-all-dev:arm64 (3.7.1-1ubuntu1) ... Setting up python2-dev (2.7.15-3) ... Setting up python3-attr (18.2.0-1) ... Setting up cython3 (0.28.4-1build1) ... Setting up libgssapi3-heimdal:arm64 (7.5.0+dfsg-2) ... Setting up python3-lib2to3 (3.7.1-1ubuntu3) ... Setting up python3-distutils (3.7.1-1ubuntu3) ... Setting up python (2.7.15-3) ... Setting up python3-atomicwrites (1.1.5-2) ... Setting up libpython-dev:arm64 (2.7.15-3) ... Setting up python-atomicwrites (1.1.5-2) ... Setting up python-attr (18.2.0-1) ... Setting up python3-py (1.7.0-1) ... Setting up python-dev (2.7.15-3) ... Setting up python3-pytest (3.6.4-1) ... Setting up python-pluggy (0.8.0-1) ... Setting up libpython-all-dev:arm64 (2.7.15-3) ... Setting up python-pkg-resources (40.5.0-1) ... Setting up cython (0.28.4-1build1) ... Setting up python-six (1.11.0-2) ... Setting up libldap-2.4-2:arm64 (2.4.46+dfsg-5ubuntu2) ... Setting up python-funcsigs (1.0.2-4) ... Setting up python3-setuptools (40.5.0-1) ... Setting up dh-python (3.20180927ubuntu2) ... Setting up python-all (2.7.15-3) ... Setting up python-setuptools (40.5.0-1) ... Setting up libcurl3-gnutls:arm64 (7.61.0-1ubuntu2.2) ... Setting up python-py (1.7.0-1) ... Setting up python-more-itertools (4.2.0-1) ... Setting up python3-dev (3.7.1-1ubuntu1) ... Setting up python-pytest (3.6.4-1) ... Setting up python-all-dev (2.7.15-3) ... Setting up python3-all (3.7.1-1ubuntu1) ... Setting up tabix (1.9-3) ... Setting up libhts2:arm64 (1.9-3) ... Setting up python3-all-dev (3.7.1-1ubuntu1) ... Setting up libhts-dev:arm64 (1.9-3) ... Setting up samtools (1.9-1) ... Setting up bcftools (1.9-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up dh-strip-nondeterminism (0.044-1) ... Setting up dh-exec (0.23build1) ... Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-138-generic arm64 (aarch64) Toolchain package versions: binutils_2.31.1-7ubuntu1 dpkg-dev_1.19.0.5ubuntu5 g++-8_8.2.0-9ubuntu1 gcc-8_8.2.0-9ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 bcftools_1.9-1 binutils_2.31.1-7ubuntu1 binutils-aarch64-linux-gnu_2.31.1-7ubuntu1 binutils-common_2.31.1-7ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-9ubuntu1 cython_0.28.4-1build1 cython3_0.28.4-1build1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23build1 dh-python_3.20180927ubuntu2 dh-strip-nondeterminism_0.044-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.0.5ubuntu5 dpkg-dev_1.19.0.5ubuntu5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-9ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-9ubuntu1 gcc-8-base_8.2.0-9ubuntu1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-2ubuntu1 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.21 init_1.55 init-system-helpers_1.55 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2 libassuan0_2.5.1-2 libatomic1_8.2.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-7ubuntu1 libblkid1_2.32-0.1ubuntu2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9ubuntu1 libcom-err2_1.44.4-2 libcomerr2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libcurl3-gnutls_7.61.0-1ubuntu2.2 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.0.5ubuntu5 libelf1_0.170-0.5.0ubuntu1 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.044-1 libgcc-8-dev_8.2.0-9ubuntu1 libgcc1_1:8.2.0-9ubuntu1 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.18.1-1 libgdbm5_1.14.1-6 libgdbm6_1.18.1-1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.6.4-2ubuntu1 libgomp1_8.2.0-9ubuntu1 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16-2ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2 libhcrypto4-heimdal_7.5.0+dfsg-2 libheimbase1-heimdal_7.5.0+dfsg-2 libheimntlm0-heimdal_7.5.0+dfsg-2 libhogweed4_3.4-1 libhts-dev_1.9-3 libhts2_1.9-3 libhx509-5-heimdal_7.5.0+dfsg-2 libicu60_60.2-6ubuntu1 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-2 libitm1_8.2.0-9ubuntu1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu1.1 libkrb5-26-heimdal_7.5.0+dfsg-2 libkrb5-3_1.16-2ubuntu1 libkrb5support0_1.16-2ubuntu1 libldap-2.4-2_2.4.46+dfsg-5ubuntu2 libldap-common_2.4.46+dfsg-5ubuntu2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-9ubuntu1 liblz4-1_1.8.2-1ubuntu1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnghttp2-14_1.34.0-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.0-3 libpipeline1_1.5.0-2 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libpython-all-dev_2.7.15-3 libpython-dev_2.7.15-3 libpython-stdlib_2.7.15-3 libpython2-dev_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7_2.7.15-4ubuntu4 libpython2.7-dev_2.7.15-4ubuntu4 libpython2.7-minimal_2.7.15-4ubuntu4 libpython2.7-stdlib_2.7.15-4ubuntu4 libpython3-all-dev_3.7.1-1ubuntu1 libpython3-dev_3.7.1-1ubuntu1 libpython3-stdlib_3.7.1-1ubuntu1 libpython3.7_3.7.1-1 libpython3.7-dev_3.7.1-1 libpython3.7-minimal_3.7.1-1 libpython3.7-stdlib_3.7.1-1 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.25.3-1 libss2_1.44.4-2 libssl1.1_1.1.1-1ubuntu2 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 libsystemd0_239-7ubuntu10.1 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_8.2.0-9ubuntu1 libubsan1_8.2.0-9ubuntu1 libudev1_239-7ubuntu10.1 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1ubuntu2 libwind0-heimdal_7.5.0+dfsg-2 libxml2_2.9.4+dfsg1-7ubuntu2 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-all_2.7.15-3 python-all-dev_2.7.15-3 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-dev_2.7.15-3 python-funcsigs_1.0.2-4 python-minimal_2.7.15-3 python-more-itertools_4.2.0-1 python-pkg-resources_40.5.0-1 python-pluggy_0.8.0-1 python-py_1.7.0-1 python-pytest_3.6.4-1 python-setuptools_40.5.0-1 python-six_1.11.0-2 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-4ubuntu4 python2.7-dev_2.7.15-4ubuntu4 python2.7-minimal_2.7.15-4ubuntu4 python3_3.7.1-1ubuntu1 python3-all_3.7.1-1ubuntu1 python3-all-dev_3.7.1-1ubuntu1 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.1-1ubuntu1 python3-distutils_3.7.1-1ubuntu3 python3-lib2to3_3.7.1-1ubuntu3 python3-minimal_3.7.1-1ubuntu1 python3-more-itertools_4.2.0-1 python3-pkg-resources_40.5.0-1 python3-pluggy_0.8.0-1 python3-py_1.7.0-1 python3-pytest_3.6.4-1 python3-setuptools_40.5.0-1 python3-six_1.11.0-2 python3.7_3.7.1-1 python3.7-dev_3.7.1-1 python3.7-minimal_3.7.1-1 readline-common_7.0-5 samtools_1.9-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu10.1 systemd-sysv_239-7ubuntu10.1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tabix_1.9-3 tar_1.30+dfsg-2 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Sep 14 21:03:17 2018 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.1+ds-1.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.15.1+ds dpkg-source: info: unpacking python-pysam_0.15.1+ds.orig.tar.gz dpkg-source: info: unpacking python-pysam_0.15.1+ds-1.debian.tar.xz dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying skip_test_needing_missing_data.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15634522 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15634522 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15634522 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.1+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build python-pysam-0.15.1+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-0.15.1+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-pysam-0.15.1+ds' dh_auto_clean I: pybuild base:217: 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-0.15.1+ds/.pybuild/cpython2_2.7_pysam/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:217: python3.7 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-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds' dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: 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:217: python3.7 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:217: /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-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -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/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-2.7/samtools creating build/temp.linux-arm64-2.7/samtools/lz4 aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-arm64-2.7/pysam/libcsamtools.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_markdup.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-arm64-2.7/samtools/samtools.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/tmp_file.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_utils.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-arm64-2.7/samtools/lz4/lz4.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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcsamtools.o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_reheader.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/sample.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_markdup.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/padding.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-2.7/samtools/samtools.pysam.o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-2.7/samtools/faidx.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/sam_header.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-2.7/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c building 'pysam.libcbcftools' 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-arm64-2.7/pysam/libcbcftools.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfsort.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 In function ‘init_data’, inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5: bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from bcftools/vcfcall.c.pysam.c:34: bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’: /usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur; ^~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/smpl_ilist.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/csq.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam_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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/hclust.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/regidx.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bcftools.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/mpileup.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bin.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfbuf.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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 -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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbcftools.o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-2.7/bcftools/csq.c.pysam.o build/temp.linux-arm64-2.7/bcftools/reheader.c.pysam.o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-2.7/bcftools/hclust.c.pysam.o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o build/temp.linux-arm64-2.7/bcftools/regidx.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mcall.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/convert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bcftools.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcutils.pyx to pysam/libcutils.c building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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:6113:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] bcftools_set_stderr(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stderr pysam/libcutils.c:6285:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] bcftools_set_stdout_fn(__pyx_t_13); ^~~~~~~~~~~~~~~~~~~~~~ samtools_set_stdout_fn pysam/libcutils.c:6296:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] bcftools_set_stdout(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stdout pysam/libcutils.c:7128:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] bcftools_set_optind(1); ^~~~~~~~~~~~~~~~~~~ samtools_set_optind pysam/libcutils.c:7207:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ samtools_main pysam/libcutils.c:7276:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] bcftools_unset_stderr(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stderr pysam/libcutils.c:7312:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] bcftools_unset_stdout(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:11374:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5812:7: 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 -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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -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 -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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:30109:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ~^~~~~~~~~~~~~~~~~~~ In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:573: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28362:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(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:13970:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-arm64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcsamfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 In file included from /usr/include/python2.7/Python.h:83, from pysam/libcalignedsegment.c:4: pysam/libcalignedsegment.c: In function ‘initlibcalignedsegment’: /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libcalignedsegment.c:2140:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libcalignedsegment.c:58727:5: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyDict_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libcalignedsegment.c:2140:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libcalignedsegment.c:58743:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14246:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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:8706:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13977:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 975, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14009:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14379:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libctabix.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcfaidx.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:33142:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:572: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ 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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbgzf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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 In file included from /usr/include/python2.7/Python.h:83, from pysam/libctabixproxies.c:4: pysam/libctabixproxies.c: In function ‘initlibctabixproxies’: /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19208:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19211:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19238:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19266:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19320:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19323:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19380:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19434:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19437:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19468:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19486:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19504:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19522:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19540:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyFloat_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19558:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19576:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19594:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19612:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19630:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19648:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19666:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19689:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19707:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyInt_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19725:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19743:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19761:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19779:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19797:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19815:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ /usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((PyObject*)(op))->ob_refcnt++) ~^~~~~~~~~~~~~~~~ pysam/libctabixproxies.c:1239:27: note: in expansion of macro ‘Py_INCREF’ #define __Pyx_INCREF(r) Py_INCREF(r) ^~~~~~~~~ pysam/libctabixproxies.c:19833:3: note: in expansion of macro ‘__Pyx_INCREF’ __Pyx_INCREF(((PyObject *)(&PyString_Type))); ^~~~~~~~~~~~ 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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN 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-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -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.71’: pysam/libcvcf.c:24714:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __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-NhXHOx/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcvcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN I: pybuild base:217: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/samtools.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/utils.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/config.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/version.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libchtslib.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools creating /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 Fixing /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-arm64-3.7 creating build/temp.linux-arm64-3.7/pysam aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.7/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 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libchtslib.o build/temp.linux-arm64-3.7/pysam/htslib_util.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-3.7/samtools creating build/temp.linux-arm64-3.7/samtools/lz4 aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-arm64-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_markdup.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-arm64-3.7/samtools/samtools.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/tmp_file.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_utils.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-arm64-3.7/samtools/lz4/lz4.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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcsamtools.o build/temp.linux-arm64-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-3.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_view.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-3.7/samtools/sample.c.pysam.o build/temp.linux-arm64-3.7/samtools/stats.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-3.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-3.7/samtools/dict.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-3.7/samtools/cut_target.c.pysam.o build/temp.linux-arm64-3.7/samtools/padding.c.pysam.o build/temp.linux-arm64-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-3.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-3.7/samtools/samtools.pysam.o build/temp.linux-arm64-3.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-3.7/samtools/faidx.c.pysam.o build/temp.linux-arm64-3.7/samtools/phase.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_index.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_header.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-3.7/samtools/lz4/lz4.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension creating build/temp.linux-arm64-3.7/bcftools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-arm64-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfsort.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/smpl_ilist.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/csq.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam_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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/hclust.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/regidx.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/mcall.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bcftools.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/mpileup.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfmerge.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bin.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfbuf.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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-3.7/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 -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcmp.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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbcftools.o build/temp.linux-arm64-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-3.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-3.7/bcftools/csq.c.pysam.o build/temp.linux-arm64-3.7/bcftools/reheader.c.pysam.o build/temp.linux-arm64-3.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-3.7/bcftools/hclust.c.pysam.o build/temp.linux-arm64-3.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.7/bcftools/main.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-3.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-3.7/bcftools/em.c.pysam.o build/temp.linux-arm64-3.7/bcftools/regidx.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-3.7/bcftools/mcall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/version.c.pysam.o build/temp.linux-arm64-3.7/bcftools/prob1.c.pysam.o build/temp.linux-arm64-3.7/bcftools/convert.c.pysam.o build/temp.linux-arm64-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bcftools.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/HMM.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcmp.c.pysam.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-arm64-3.7/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:6113:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] bcftools_set_stderr(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stderr pysam/libcutils.c:6285:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] bcftools_set_stdout_fn(__pyx_t_13); ^~~~~~~~~~~~~~~~~~~~~~ samtools_set_stdout_fn pysam/libcutils.c:6296:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] bcftools_set_stdout(__pyx_t_10); ^~~~~~~~~~~~~~~~~~~ samtools_set_stdout pysam/libcutils.c:7128:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] bcftools_set_optind(1); ^~~~~~~~~~~~~~~~~~~ samtools_set_optind pysam/libcutils.c:7207:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ samtools_main pysam/libcutils.c:7276:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] bcftools_unset_stderr(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stderr pysam/libcutils.c:7312:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] bcftools_unset_stdout(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:480:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5812:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-arm64-3.7/pysam/pysam_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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcutils.o build/temp.linux-arm64-3.7/pysam/pysam_util.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcsamtools.cpython-37m-aarch64-linux-gnu -lcbcftools.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-3.7/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:30109:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ~^~~~~~~~~~~~~~~~~~~ In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:573: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28362:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(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:13970:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcalignmentfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-arm64-3.7/pysam/libcsamfile.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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcsamfile.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14246:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcalignedsegment.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-arm64-3.7/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:8706:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13977:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 975, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14009:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14379:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) ^~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libctabix.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-arm64-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcfaidx.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-arm64-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:33142:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:572: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-arm64-3.7/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 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbgzf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-arm64-3.7/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 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libctabixproxies.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/python-pysam-0.15.1+ds/samtools -I/<>/python-pysam-0.15.1+ds/samtools/lz4 -I/<>/python-pysam-0.15.1+ds/bcftools -I/<>/python-pysam-0.15.1+ds/pysam -I/<>/python-pysam-0.15.1+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-arm64-3.7/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.73’: pysam/libcvcf.c:24714:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/python-pysam-0.15.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcvcf.o -L/<>/python-pysam-0.15.1+ds/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-pysam-0.15.1+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.15.1+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 gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view -bS with_md.sam > with_md.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS 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 ex4.sam > ex4.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam samtools view -bS ex5.sam > ex5.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 ex6.sam > ex6.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 example_dash_in_chr.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 ex4.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index example_reverse_complement.bam samtools index ex5.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 ex6.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 rm with_md.sam make[2]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/python-pysam-0.15.1+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 < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_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 gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_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-0.15.1+ds/tests/cbcf_data' dh_auto_test I: pybuild base:217: cd /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests ============================= test session starts ============================== platform linux2 -- Python 2.7.15+, pytest-3.6.4, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python2.7 cachedir: ../../../.pytest_cache rootdir: /<>/python-pysam-0.15.1+ds, inifile: setup.cfg collecting ... collected 920 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== .pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: http://doc.pytest.org/en/latest/warnings.html ============= 903 passed, 17 skipped, 1 warnings in 112.97 seconds ============= I: pybuild base:217: cd /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build; python3.7 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.7.1, pytest-3.6.4, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python3.7 cachedir: ../../../.pytest_cache rootdir: /<>/python-pysam-0.15.1+ds, inifile: setup.cfg collecting ... collected 924 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== .pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: http://doc.pytest.org/en/latest/warnings.html ============= 914 passed, 10 skipped, 1 warnings in 121.85 seconds ============= make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /<>/python-pysam-0.15.1+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-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) 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/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7 creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/__init__.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bedidx.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_stream.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/csamtools_util.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/htslib_util.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_util.h -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.py -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.pyc -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython2_2.7_pysam/build/log.txt -> /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.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' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/win/*.c' warning: no files found matching 'htslib/win/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.15.1+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.15.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/python-pysam-0.15.1+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-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/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-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7 creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sample.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_header.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/config.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bedidx.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/version.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/prob1.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/regidx.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/mw.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kmin.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/HMM.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kheap.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/call.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bin.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/config.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/filter.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/convert.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/version.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/hclust.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_stream.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/csamtools_util.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/cbcftools_util.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/htslib_util.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam creating /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/utils.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/Pileup.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/__init__.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/bcftools.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/version.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/samtools.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/config.cpython-37.pyc -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_util.h -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-aarch64-linux-gnu.so -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.pxd -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /<>/python-pysam-0.15.1+ds/.pybuild/cpython3_3.7_pysam/build/log.txt -> /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/Pileup.py to Pileup.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/bcftools.py to bcftools.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/samtools.py to samtools.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/utils.py to utils.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/config.py to config.cpython-37.pyc byte-compiling /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/version.py to version.cpython-37.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' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/win/*.c' warning: no files found matching 'htslib/win/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /<>/python-pysam-0.15.1+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam-0.15.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>/python-pysam-0.15.1+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[2]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/python-pysam-0.15.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz make[1]: Leaving directory '/<>/python-pysam-0.15.1+ds' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:329: renaming libcalignedsegment.so to libcalignedsegment.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcalignmentfile.so to libcalignmentfile.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcbcf.so to libcbcf.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcbcftools.so to libcbcftools.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcbgzf.so to libcbgzf.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcfaidx.so to libcfaidx.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libchtslib.so to libchtslib.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcsamfile.so to libcsamfile.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcsamtools.so to libcsamtools.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libctabix.so to libctabix.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libctabixproxies.so to libctabixproxies.aarch64-linux-gnu.so I: dh_python2 fs:329: renaming libcutils.so to libcutils.aarch64-linux-gnu.so I: dh_python2 fs:329: 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_missing -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild 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 python3-pysam: unused substitution variable ${python3:Provides} 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:Versions} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing python-pysam-dbgsym (in debian/.debhelper/python-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam (in debian/python-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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 dpkg-deb: building package 'python-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pysam/python-pysam-dbgsym_0.15.1+ds-1_arm64.deb'. 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_0.15.1+ds-1_arm64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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 dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.15.1+ds-1_arm64.deb'. pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam Renaming python-pysam-dbgsym_0.15.1+ds-1_arm64.deb to python-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb 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_0.15.1+ds-1_arm64.deb'. Renaming python3-pysam-dbgsym_0.15.1+ds-1_arm64.deb to python3-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-pysam_0.15.1+ds-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build python-pysam-0.15.1+ds dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181110-0212 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.15.1+ds-1_arm64.changes: --------------------------------------- Format: 1.8 Date: Fri, 14 Sep 2018 10:44:51 +0200 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: arm64 Version: 0.15.1+ds-1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steffen Moeller 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 (0.15.1+ds-1) unstable; urgency=medium . * Team upload. . * New upstream version. - Removes autogenerated config.h - [many thanks!] https://github.com/pysam-developers/pysam/issues/714 - Explicit compatibility with Python 3.7 * Removed patch skipping test that complained on missing file Checksums-Sha1: bbb7d63c8ccef3866cababded0ab5af65c02ccca 5742628 python-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb 9cb30bfc5d87afc876eb6032f5985e0a8aed19cc 8840 python-pysam_0.15.1+ds-1_arm64.buildinfo 2fd0303e84431d1e9113550c677dfba0b2dfb626 1412776 python-pysam_0.15.1+ds-1_arm64.deb 0d75c2c33160314db895b2f71508f74607d2658b 6567352 python3-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb 2fef179dffb255f1f7e4a47c4e2cf175bb9e1ea0 1437584 python3-pysam_0.15.1+ds-1_arm64.deb Checksums-Sha256: 4d9253491c3bafc2bebe07d5302b7a98b26589ae12dfeaafc2b2fccda8bdbb27 5742628 python-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb c6814f800a1caa1abb7aa98dce4def23df2b1afb96cbc880d01d9a6dfa76f53f 8840 python-pysam_0.15.1+ds-1_arm64.buildinfo 03bbdee463add4c7aa6cd28789eb92e5cc814cb31d64f9dca3baa7df512ce1d7 1412776 python-pysam_0.15.1+ds-1_arm64.deb 2d0ce09555d882fc1cea33e2438ded8f27c5791e05e45d71f4209b5bbdc6bb16 6567352 python3-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb 9b4af99d545df4aa7b862be50cc41c070150c084b869e4b629f392f62d9be665 1437584 python3-pysam_0.15.1+ds-1_arm64.deb Files: 70742842bad951e7c88969491bd1e633 5742628 debug optional python-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb 85390e56b1f8a29accc35db7a3785c9e 8840 python optional python-pysam_0.15.1+ds-1_arm64.buildinfo 78e450519660d824c7c6c30cc0c83310 1412776 python optional python-pysam_0.15.1+ds-1_arm64.deb b00a5dfc7ae3371d45bd5c9c1653933e 6567352 debug optional python3-pysam-dbgsym_0.15.1+ds-1_arm64.ddeb 724176a5175c780f1a71958ba27960e0 1437584 python optional python3-pysam_0.15.1+ds-1_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pysam_0.15.1+ds-1_arm64.deb ---------------------------------- new debian package, version 2.0. size 1412776 bytes: control archive=3296 bytes. 774 bytes, 16 lines control 8612 bytes, 90 lines md5sums 162 bytes, 9 lines * postinst #!/bin/sh 263 bytes, 14 lines * prerm #!/bin/sh Package: python-pysam Version: 0.15.1+ds-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5549 Depends: libc6 (>= 2.17), libhts2 (>= 1.9), zlib1g (>= 1:1.1.4), python (<< 2.8), python (>= 2.7~), python:any (<< 2.8), python:any (>= 2.7~) Section: python Priority: optional Homepage: http://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2) 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/doc/python-pysam/copyright drwxr-xr-x root/root 0 2018-09-14 08:44 ./usr/share/lintian/ drwxr-xr-x root/root 0 2018-09-14 08:44 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 211 2018-07-28 22:37 ./usr/share/lintian/overrides/python-pysam python3-pysam_0.15.1+ds-1_arm64.deb ----------------------------------- new debian package, version 2.0. size 1437584 bytes: control archive=3392 bytes. 768 bytes, 17 lines control 8597 bytes, 90 lines md5sums 252 bytes, 12 lines * postinst #!/bin/sh 401 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.15.1+ds-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5593 Depends: libc6 (>= 2.17), libhts2 (>= 1.9), zlib1g (>= 1:1.1.4), python3 (<< 3.8), python3 (>= 3.7~), python3:any 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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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 219792 Build-Time: 1434 Distribution: disco-proposed Host Architecture: arm64 Install-Time: 48 Job: python-pysam_0.15.1+ds-1.dsc Machine Architecture: arm64 Package: python-pysam Package-Time: 1484 Source-Version: 0.15.1+ds-1 Space: 219792 Status: successful Version: 0.15.1+ds-1 -------------------------------------------------------------------------------- Finished at 20181110-0212 Build needed 00:24:44, 219792k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=arm64 PACKAGEBUILD-15634522 Scanning for processes to kill in build PACKAGEBUILD-15634522