I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 13 15:52:55 -12 2025 I: pbuilder-time-stamp: 1760413975 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pysam_0.22.1+ds-2.dsc] I: copying [./python-pysam_0.22.1+ds.orig.tar.xz] I: copying [./python-pysam_0.22.1+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 29 11:37:25 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.22.1+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting python-pysam in python-pysam-0.22.1+ds dpkg-source: info: unpacking python-pysam_0.22.1+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.22.1+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying clean_less dpkg-source: info: applying skip-test-on-32-bit.patch dpkg-source: info: applying htslib-1.20.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2693087/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b6d6ae24b25f45688e008acd79f0355f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2693087' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.u5xuVE8u/pbuilderrc_EHKr --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u5xuVE8u/b1 --logfile b1/build.log python-pysam_0.22.1+ds-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2693087/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19735 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14~); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bsdextrautils{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnsl2{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tabix{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix python3-gffutils python3-matplotlib python3-pygments wget 0 packages upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 57.4 MB of archives. After unpacking 225 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1 [9588 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1 [27.6 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.9.1-2 [470 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.20-2 [760 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-1 [2449 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-1 [42.2 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.1-1 [10.2 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240824 [109 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b4 [313 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.20.0-1+b1 [583 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.6-2 [439 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2 [439 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2 [123 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2 [208 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b2 [98.0 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1 [1316 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.6-2 [1381 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.63.0-1 [115 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1 [86.5 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1 [77.4 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b4 [67.7 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-1 [2742 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.0-7 [357 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.9.1-2 [582 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.21-1 [55.8 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.5-1 [9820 B] Get: 117 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.5-1 [1068 B] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.5-1 [1044 B] Get: 119 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.5-1 [26.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.5-1 [1068 B] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.2-1 [249 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-1 [483 kB] Fetched 57.4 MB in 2s (35.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19735 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21127 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1_amd64.deb ... Unpacking python3 (3.12.5-1) ... Selecting previously unselected package sensible-utils. 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Selecting previously unselected package libpsl-dev:amd64. Preparing to unpack .../077-libpsl-dev_0.21.2-1.1_amd64.deb ... Unpacking libpsl-dev:amd64 (0.21.2-1.1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../078-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package librtmp-dev:amd64. Preparing to unpack .../079-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../080-libssl-dev_3.3.2-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.3.2-1) ... Selecting previously unselected package libssh2-1-dev:amd64. Preparing to unpack .../081-libssh2-1-dev_1.11.0-7_amd64.deb ... Unpacking libssh2-1-dev:amd64 (1.11.0-7) ... Selecting previously unselected package libzstd-dev:amd64. 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Selecting previously unselected package libjs-jquery. Preparing to unpack .../088-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../089-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../090-libjs-sphinxdoc_7.4.7-3_all.deb ... Unpacking libjs-sphinxdoc (7.4.7-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../091-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libpython3.12t64:amd64. Preparing to unpack .../092-libpython3.12t64_3.12.6-1_amd64.deb ... Unpacking libpython3.12t64:amd64 (3.12.6-1) ... Selecting previously unselected package libpython3.12-dev:amd64. 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Preparing to unpack .../105-tabix_1.20+ds-1_amd64.deb ... Unpacking tabix (1.20+ds-1) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.6-2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-5) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libpsl-dev:amd64 (0.21.2-1.1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 14 03:53:30 UTC 2025. Universal Time is now: Tue Oct 14 03:53:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.20.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libexpat1-dev:amd64 (2.6.3-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libssl-dev:amd64 (3.3.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Setting up libdeflate-dev:amd64 (1.21-1) ... Setting up tabix (1.20+ds-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.0-7) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.63.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up bcftools (1.20-2) ... Setting up debhelper (13.20) ... Setting up libcurl4-gnutls-dev:amd64 (8.9.1-2) ... Setting up samtools (1.20-3) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up libpython3-stdlib:amd64 (3.12.5-1) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Setting up python3 (3.12.5-1) ... Setting up libpython3.12-dev:amd64 (3.12.6-1) ... Setting up python3-zipp (3.20.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.1-1) ... Setting up python3.12-dev (3.12.6-1) ... Setting up cython3 (3.0.11+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:amd64 (3.12.5-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.2-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.5-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up libpython3-all-dev:amd64 (3.12.5-1) ... Setting up python3-dev (3.12.5-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.5-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up dh-python (6.20240824) ... Processing triggers for libc-bin (2.40-2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-pysam-0.22.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pysam_0.22.1+ds-2_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.22.1+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 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 -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/bcftools.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/config.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/Pileup.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/samtools.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/version.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/__init__.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/utils.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam creating /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' warning: no files found matching 'win32/*.[ch]' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/csamtools_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/htslib_util.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/htslib_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignedsegment.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbgzf.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbgzf.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/py.typed -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/pysam_stream.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/pysam_util.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/pysam_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/version.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/version.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam creating /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/LICENSE -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/README -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/amplicon_stats.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam2depth.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_addrprg.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_aux.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_cat.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_color.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_consensus.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_fastq.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_flags.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_import.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_index.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_markdup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_mate.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_md.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plcmd.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_quickcheck.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_reheader.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdupse.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_samples.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_sort.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_split.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_stat.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamshuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamtk.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedcov.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/coverage.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/coverage.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cram_size.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cut_target.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/dict.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/dict.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/faidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/faidx.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/padding.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/padding.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/phase.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/phase.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reference.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reference.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reset.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reset.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_opts.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_utils.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_utils.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_view.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sample.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sample.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/splaysort.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats_isize.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/tmp_file.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/version.sh -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools creating /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/config.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools creating /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/HMM.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/LICENSE -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/README -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/abuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bin.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ccall.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cigar_state.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cols.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/consensus.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/convert.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/csq.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dist.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/em.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/em.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/extsort.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/filter.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gff.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gff.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gvcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hclust.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kmin.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/main.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/main.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mcall.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mpileup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ploidy.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/prob1.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/regidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/reheader.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/str_finder.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tabix.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfannotate.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcall.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcnv.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconcat.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconvert.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcffilter.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfhead.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfindex.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfisec.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfmerge.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfnorm.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfplugin.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfquery.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfroh.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsom.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsort.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfstats.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfview.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcmp.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/version.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/version.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/version.sh -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools running build_ext Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/pysam x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-312/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/htslib_util.o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-cpython-312/samtools creating build/temp.linux-x86_64-cpython-312/samtools/lz4 x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/reference.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/reset.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/tmp_file.c.pysam.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-cpython-312/bcftools x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/gff.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ bcftools/vcfmerge.c.pysam.c:866:27: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 866 | ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/gff.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-x86_64-cpython-312/pysam/libcbcftools.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcutils.c -o build/temp.linux-x86_64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-x86_64-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcutils.o build/temp.linux-x86_64-cpython-312/pysam/pysam_util.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcsamtools.cpython-312-x86_64-linux-gnu -lcbcftools.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx:2567:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2616:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:20533:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20533 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:37169:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37169 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcalignmentfile.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcsamfile.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignedsegment.pyx:760:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: pysam/libcalignedsegment.pyx:760:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcalignedsegment.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libctabix.c -o build/temp.linux-x86_64-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libctabix.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcfaidx.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcbcf.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:85926:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85926 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:80602:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80602 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:44311:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44311 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44337:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44337 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:80297:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80297 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcbcf.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcbgzf.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbgzf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libctabixproxies.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/python-pysam-0.22.1+ds/pysam -I/usr/include -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools -I/build/reproducible-path/python-pysam-0.22.1+ds/samtools/lz4 -I/build/reproducible-path/python-pysam-0.22.1+ds/bcftools -I/build/reproducible-path/python-pysam-0.22.1+ds -I/usr/include/python3.12 -c pysam/libcvcf.c -o build/temp.linux-x86_64-cpython-312/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’: pysam/libcvcf.c:30039:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 30039 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24991:10: note: ‘__pyx_v_qual’ was declared here 24991 | double __pyx_v_qual; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-pysam-0.22.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pysam/libcvcf.o -L/build/reproducible-path/python-pysam-0.22.1+ds/pysam -L/usr/lib/x86_64-linux-gnu -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/pysam_data' samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view --no-PG -bo ex2.bam ex2.sam samtools index ex2.bam samtools calmd --no-PG --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 --no-PG -bo with_md.bam with_md.sam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view --no-PG -bu -o uncompressed.bam ex2.sam samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam samtools view --no-PG -bo MM-double.bam MM-double.sam samtools view --no-PG -bo MM-multi.bam MM-multi.sam samtools view --no-PG -bo MM-orient.bam MM-orient.sam samtools view --no-PG -bo ex10.bam ex10.sam samtools view --no-PG -bo ex3.bam ex3.sam samtools view --no-PG -bo ex4.bam ex4.sam samtools view --no-PG -bo ex5.bam ex5.sam samtools view --no-PG -bo ex6.bam ex6.sam samtools view --no-PG -bo ex8.bam ex8.sam samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam samtools view --no-PG -bo example_btag.bam example_btag.sam samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam touch tmp.list samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view --no-PG -bo issue100.bam issue100.sam samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam samtools view --no-PG -bo softclip.bam softclip.sam samtools view --no-PG -bo tag_bug.bam tag_bug.sam samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam samtools view --no-PG -bo test_query_position.bam test_query_position.sam samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam samtools index MM-chebi.bam samtools index MM-double.bam samtools index MM-multi.bam samtools index MM-orient.bam samtools index ex10.bam samtools index ex3.bam samtools index ex4.bam samtools index ex5.bam samtools index ex6.bam samtools index ex8.bam samtools index ex9_fail.bam samtools index ex9_nofail.bam samtools index ex_spliced.bam samtools index example_aligned_pairs.bam samtools index example_btag.bam samtools index example_dash_in_chr.bam samtools index example_empty_header.bam samtools index example_empty_with_header.bam samtools index example_reverse_complement.bam samtools index example_unmapped_reads_no_sq.bam samtools index issue100.bam samtools index rg_with_tab.bam samtools index softclip.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index test_query_position.bam samtools index test_unaligned.bam samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam 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 dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 records in 1+0 records out 122288 bytes (122 kB, 119 KiB) copied, 0.000245643 s, 498 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo 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 touch all.stamp rm with_md.sam make[2]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/cbcf_data' bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < example_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 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_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.vcf.gz # create csi index bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.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 < 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 bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.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 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_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.bcf bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.bcf bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.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 missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf touch all.stamp make[2]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/cbcf_data' dh_auto_test I: pybuild base:311: cd /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache rootdir: /build/reproducible-path/python-pysam-0.22.1+ds configfile: setup.cfg plugins: typeguard-4.3.0 collecting ... collected 951 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::testUpdateQual PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md 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_padding_with_seq 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::TestBaseModifications::testChebi PASSED tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED tests/AlignedSegment_test.py::TestBaseModifications::testOrient 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 /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_c6qbl1fz PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_gabxvbdp' /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_gabxvbdp PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_tqm1_dig PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_16n6o78e PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_y5_cm08v' /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_y5_cm08v PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_elg4wgoj 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 SKIPPED 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::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" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header 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_block] Failed to read BGZF block data at offset 105176 expected 17578 bytes; hread returned 17094 [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_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::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" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_q1y17ylv.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_set_sample_alleles PASSED tests/compile_test.py::test_bam SKIPPED (no pyximport) tests/compile_test.py::test_gtf SKIPPED (no pyximport) tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error 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 (skipping us...) tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 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::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_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_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_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_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_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_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_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_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_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_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_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_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_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_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_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_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_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_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::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::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] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] 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_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_dict2] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_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_dict2] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:249843 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] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 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_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] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' 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] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting 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] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GQ' at chr1:1281168 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_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_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: #CHROM POS ID REF ALT QUAL FILTER INFO PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing 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] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing 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_dict2] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) 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_dict2] FORMAT 'GT' at 20:249843 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_dict2] FORMAT 'GT' at 20:676148 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::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::TestBED::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList 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::testAssignmentToTargetList 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::testAssignmentToTargetList 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_3.12_pysam/build/tests/samtools_test.py::SamtoolsTest::testStatements .pybuild/cpython3_3.12_pysam/build/tests/samtools_test.py::PysamTest::testStatements /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/tests/samtools_test.py:137: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.20 warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================= 938 passed, 13 skipped, 2 warnings in 21.99s ================= make[1]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pysam/config.py -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'win32/*.[ch]' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/libcalignedsegment.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbgzf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam copying samtools/config.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools_config_vars.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying bcftools/config.h -> /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools running build_ext creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12 creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbgzf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/version.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/version.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbgzf.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/bcftools.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/config.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/ccall.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/str_finder.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/prob1.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/consensus.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/cigar_state.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfannotate.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/cols.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/gff.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfconcat.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfconvert.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/extsort.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bcftools.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/version.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfcnv.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfbuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/LICENSE -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/filter.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/ploidy.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/call.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/regidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/HMM.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/gff.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bin.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfview.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bcftools.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/reheader.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/main.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfcall.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfnorm.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcffilter.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcmp.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf_indel.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/str_finder.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam_sample.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/abuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/csq.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfconvert.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfsort.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/version.sh -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/ccall.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfview.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/gvcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/HMM.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/consensus.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/kheap.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfindex.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/gvcf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfcall.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/convert.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/str_finder.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/version.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/utlist.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf_iaux.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcffilter.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/abuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfmerge.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfplugin.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/kmin.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/read_consensus.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/filter.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/dist.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/dist.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/regidx.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/main.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcmp.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/ploidy.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/cols.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/extsort.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/em.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/abuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/variantkey.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/dbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/dist.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfcnv.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/gff.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/HMM.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/rbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfroh.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/mcall.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfisec.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/gvcf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/hex.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/cols.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfgtcheck.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/hclust.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfroh.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/extsort.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfquery.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/mw.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/read_consensus.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/read_consensus.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfhead.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam_sample.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfquery.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/prob1.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/reheader.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/regidx.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/tabix.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfsom.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/convert.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcmp.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfannotate.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfbuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfindex.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfnorm.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/mpileup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/filter.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfconcat.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/kmin.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bin.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/smpl_ilist.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/config.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/mpileup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/bin.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfmerge.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/csq.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/mcall.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/tabix.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/hclust.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/convert.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/ploidy.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/em.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfsort.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/prob1.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfstats.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfplugin.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/README -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfsom.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/hclust.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfhead.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/kmin.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/tsv2vcf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfstats.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools/vcfisec.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/bcftools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/__init__.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_cat.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_md.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_consensus.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_sort.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_fastq.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/consensus_pileup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_lpileup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_color.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/stats_isize.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/LICENSE -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/reset.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/cut_target.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_mate.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/faidx.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/amplicon_stats.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/phase.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_flags.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_addrprg.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_markdup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_cat.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_view.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_utils.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/stats_isize.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_opts.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_samples.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/tmp_file.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_view.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/coverage.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_rmdup.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_plcmd.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/samtools.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/coverage.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_rmdup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_ampliconclip.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/version.sh -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/dict.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_aux.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam2depth.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam2depth.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/splaysort.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_sort.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_index.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/samtools.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_reheader.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_samples.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_opts.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_addrprg.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_mate.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/padding.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/consensus_pileup.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bedidx.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bedidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/stats.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bamtk.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/tmp_file.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_plcmd.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/cram_size.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bedcov.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_markdup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_lpileup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/reset.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_consensus.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_fastq.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_reheader.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/reference.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_import.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bedcov.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sample.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_split.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sample.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bedidx.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sample.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/faidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_flags.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_stat.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/amplicon_stats.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/stats_isize.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools/lz4 copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4/lz4.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools/lz4 copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4/LICENSE -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools/lz4 copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4/lz4.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools/lz4 copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4/lz4.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools/lz4 copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/dict.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_stat.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/phase.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/config.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_utils.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_quickcheck.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_color.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bamshuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_index.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_plbuf.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_plbuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bamtk.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/tmp_file.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_opts.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_md.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/cut_target.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bamshuf.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/consensus_pileup.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_import.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_split.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/padding.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_rmdupse.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/README -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/reference.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/stats.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/cram_size.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_aux.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/sam_utils.c.pysam.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/samtools copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/Pileup.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/samtools.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/version.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/pysam_util.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__init__.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/cbcftools_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/utils.py -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/pysam_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/py.typed -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/csamtools_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/pysam_stream.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam creating /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/Pileup.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/utils.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/bcftools.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/samtools.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/__pycache__/config.cpython-312.pyc -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__pycache__ copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbgzf.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.pyx -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/htslib_util.h -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcbgzf.pyi -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/htslib_util.c -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam copying /build/reproducible-path/python-pysam-0.22.1+ds/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.pxd -> /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/bcftools.py to bcftools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/config.py to config.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/include/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/Pileup.py to Pileup.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/samtools.py to samtools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam/utils.py to utils.cpython-312.pyc running install_egg_info Copying pysam.egg-info to /build/reproducible-path/python-pysam-0.22.1+ds/debian/python3-pysam/usr/lib/python3.12/dist-packages/pysam-0.22.1.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[2]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete find debian -name LICENSE -delete make[1]: Leaving directory '/build/reproducible-path/python-pysam-0.22.1+ds' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so: DWARF compression not beneficial - old size 1686044 new size 1712057 dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.22.1+ds-2_amd64.deb'. dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.22.1+ds-2_amd64.deb'. dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.22.1+ds-2_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pysam_0.22.1+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pysam_0.22.1+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2693087 and its subdirectories I: Current time: Mon Oct 13 15:59:11 -12 2025 I: pbuilder-time-stamp: 1760414351