sbuild (Debian sbuild) 0.91.5 (17 December 2025) on carme.larted.org.uk +==============================================================================+ | htslib 1.22.1+ds2-1 (amd64) Sun, 26 Apr 2026 23:32:37 +0000 | +==============================================================================+ Package: htslib Version: 1.22.1+ds2-1 Source Version: 1.22.1+ds2-1 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sun, 26 Apr 2026 23:32:38 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.22.1+ds2-1 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.22.1+ds2-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 26 Apr 2026 23:32:38 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [187 kB] Get:3 http://deb.debian.org/debian sid InRelease [187 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-04-26-2001.18-F-2026-04-26-2001.18.pdiff [108 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-04-26-2001.18-F-2026-04-26-2001.18.pdiff [108 kB] Get:7 http://deb.debian.org/debian sid/main Sources T-2026-04-26-2001.18-F-2026-04-26-2001.18.pdiff [30.1 kB] Get:7 http://deb.debian.org/debian sid/main Sources T-2026-04-26-2001.18-F-2026-04-26-2001.18.pdiff [30.1 kB] Fetched 639 kB in 7s (95.4 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libassuan9 libblkid1 libbsd0 liblastlog2-2 libmount1 libsmartcols1 libuuid1 util-linux 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2091 kB of archives. After this operation, 2048 B disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libsmartcols1 amd64 2.42-5 [144 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 libuuid1 amd64 2.42-5 [33.0 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libblkid1 amd64 2.42-5 [172 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmount1 amd64 2.42-5 [213 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 util-linux amd64 2.42-5 [1222 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-2+b2 [132 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 bsdutils amd64 1:2.42-5 [90.4 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libassuan9 amd64 3.0.2-2+b2 [60.7 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 liblastlog2-2 amd64 2.42-5 [23.9 kB] Fetched 2091 kB in 0s (97.1 MB/s) (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 ... 23451 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.42-5_amd64.deb ... Unpacking libsmartcols1:amd64 (2.42-5) over (2.42-4) ... Setting up libsmartcols1:amd64 (2.42-5) ... (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 ... 23451 files and directories currently installed.) Preparing to unpack .../libuuid1_2.42-5_amd64.deb ... Unpacking libuuid1:amd64 (2.42-5) over (2.42-4) ... Setting up libuuid1:amd64 (2.42-5) ... (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 ... 23451 files and directories currently installed.) Preparing to unpack .../libblkid1_2.42-5_amd64.deb ... Unpacking libblkid1:amd64 (2.42-5) over (2.42-4) ... Setting up libblkid1:amd64 (2.42-5) ... (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 ... 23451 files and directories currently installed.) Preparing to unpack .../libmount1_2.42-5_amd64.deb ... Unpacking libmount1:amd64 (2.42-5) over (2.42-4) ... Setting up libmount1:amd64 (2.42-5) ... (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 ... 23451 files and directories currently installed.) Preparing to unpack .../util-linux_2.42-5_amd64.deb ... Unpacking util-linux (2.42-5) over (2.42-4) ... Setting up util-linux (2.42-5) ... (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 ... 23451 files and directories currently installed.) Preparing to unpack .../libbsd0_0.12.2-2+b2_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-2+b2) over (0.12.2-2+b1) ... Setting up libbsd0:amd64 (0.12.2-2+b2) ... (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 ... 23451 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.42-5_amd64.deb ... Unpacking bsdutils (1:2.42-5) over (1:2.42-4) ... Preparing to unpack .../libassuan9_3.0.2-2+b2_amd64.deb ... Unpacking libassuan9:amd64 (3.0.2-2+b2) over (3.0.2-2+b1) ... Preparing to unpack .../liblastlog2-2_2.42-5_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.42-5) over (2.42-4) ... Setting up bsdutils (1:2.42-5) ... Setting up liblastlog2-2:amd64 (2.42-5) ... Setting up libassuan9:amd64 (3.0.2-2+b2) ... Processing triggers for libc-bin (2.42-15) ... +------------------------------------------------------------------------------+ | Fetch source files Sun, 26 Apr 2026 23:32:48 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/htslib_1.22.1+ds2-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 26 Apr 2026 23:32:48 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev, build-essential Filtered Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive ./ InRelease Get:2 copy:/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive ./ Release [609 B] Ign:3 copy:/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive ./ Release.gpg Get:4 copy:/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive ./ Sources [726 B] Get:5 copy:/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive ./ Packages [765 B] Fetched 2100 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhtscodecs-dev libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhtscodecs-dev libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 28.4 MB/28.7 MB of archives. After this operation, 96.9 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b2 [305 kB] Get:2 copy:/build/htslib-BlqyQO/resolver-JSI3KM/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b2 [337 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b2 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b2 [42.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-2 [242 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42-5 [99.4 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-2 [770 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.2+dfsg-0.1 [641 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-2 [1684 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2+b1 [31.0 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2+b1 [78.9 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2+b1 [336 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2+b1 [137 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-2+b1 [58.1 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-2+b1 [40.2 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-2+b1 [41.2 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-2+b1 [54.0 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-2+b1 [125 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.5-1 [59.9 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-2 [244 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.20.0~rc3-1 [402 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.24.2-1+b1 [608 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.12-3 [475 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4+b1 [103 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.2-2 [223 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2 [99.7 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.12-3 [1450 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-2+b1 [14.0 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.5-1 [80.5 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.2-1 [3019 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-2 [393 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b1 [375 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.20.0~rc3-1 [527 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2+b2 [48.3 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2+b2 [56.9 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.6-1 [3004 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Preconfiguring packages ... Fetched 28.4 MB in 0s (142 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23451 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5+b2_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5+b2) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5+b2_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5+b2) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5+b2_amd64.deb ... Unpacking file (1:5.46-5+b2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.2-2_amd64.deb ... Unpacking gettext-base (0.23.2-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.24.1-1_amd64.deb ... Unpacking groff-base (1.24.1-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.42-5_amd64.deb ... Unpacking bsdextrautils (2.42-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-6_all.deb ... Unpacking autoconf (2.72-6) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1+nmu1_all.deb ... Unpacking autotools-dev (20240727.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.18.1-4_all.deb ... Unpacking automake (1:1.18.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.2-2_all.deb ... Unpacking autopoint (0.23.2-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.4-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.4-1) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.4-1_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.4-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.31_all.deb ... Unpacking libdebhelper-perl (13.31) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-11_all.deb ... Unpacking libtool (2.5.4-11) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_22_all.deb ... Unpacking dh-autoreconf (22) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.195-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.195-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.16-4_amd64.deb ... Unpacking dwz (0.16-4) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../25-libxml2-16_2.15.2+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.2+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.2-2_amd64.deb ... Unpacking gettext (0.23.2-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.22_all.deb ... Unpacking po-debconf (1.0.22) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.31_all.deb ... Unpacking debhelper (13.31) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../30-libkrb5support0_1.22.1-2+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../31-libk5crypto3_1.22.1-2+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../32-libkeyutils1_1.6.3-6+b2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6+b2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../33-libkrb5-3_1.22.1-2+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../34-libgssapi-krb5-2_1.22.1-2+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../35-libgssrpc4t64_1.22.1-2+b1_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../36-libkadm5clnt-mit12_1.22.1-2+b1_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../37-libkdb5-10t64_1.22.1-2+b1_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../38-libkadm5srv-mit12_1.22.1-2+b1_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.22.1-2+b1) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../39-krb5-multidev_1.22.1-2+b1_amd64.deb ... Unpacking krb5-multidev:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../40-libbrotli1_1.2.0-3_amd64.deb ... Unpacking libbrotli1:amd64 (1.2.0-3) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../41-libbrotli-dev_1.2.0-3_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.2.0-3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../42-libbz2-dev_1.0.8-6+b2_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6+b2) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../43-libnghttp3-9_1.15.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.15.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../44-libngtcp2-16_1.22.1-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.22.1-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../45-libnghttp2-14_1.69.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.69.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../46-libngtcp2-crypto-gnutls8_1.22.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../47-libpsl5t64_0.21.5-1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.5-1) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../48-libssh2-1t64_1.11.1-2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-2) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../49-libcurl3t64-gnutls_8.20.0~rc3-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.20.0~rc3-1) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../50-libevent-2.1-7t64_2.1.12-stable-10+b2_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Selecting previously unselected package libunbound8:amd64. Preparing to unpack .../51-libunbound8_1.24.2-1+b1_amd64.deb ... Unpacking libunbound8:amd64 (1.24.2-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:amd64. Preparing to unpack .../52-libgnutls-dane0t64_3.8.12-3_amd64.deb ... Unpacking libgnutls-dane0t64:amd64 (3.8.12-3) ... Selecting previously unselected package libidn2-dev:amd64. Preparing to unpack .../53-libidn2-dev_2.3.8-4+b1_amd64.deb ... Unpacking libidn2-dev:amd64 (2.3.8-4+b1) ... Selecting previously unselected package libp11-kit-dev:amd64. Preparing to unpack .../54-libp11-kit-dev_0.26.2-2_amd64.deb ... Unpacking libp11-kit-dev:amd64 (0.26.2-2) ... Selecting previously unselected package libtasn1-6-dev:amd64. Preparing to unpack .../55-libtasn1-6-dev_4.21.0-2_amd64.deb ... Unpacking libtasn1-6-dev:amd64 (4.21.0-2) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../56-libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b2_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../57-libgmp-dev_2%3a6.3.0+dfsg-5+b2_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Selecting previously unselected package nettle-dev:amd64. Preparing to unpack .../58-nettle-dev_3.10.2-1+b1_amd64.deb ... Unpacking nettle-dev:amd64 (3.10.2-1+b1) ... Selecting previously unselected package libgnutls28-dev:amd64. Preparing to unpack .../59-libgnutls28-dev_3.8.12-3_amd64.deb ... Unpacking libgnutls28-dev:amd64 (3.8.12-3) ... Selecting previously unselected package libkrb5-dev:amd64. Preparing to unpack .../60-libkrb5-dev_1.22.1-2+b1_amd64.deb ... Unpacking libkrb5-dev:amd64 (1.22.1-2+b1) ... Selecting previously unselected package libldap-dev:amd64. Preparing to unpack .../61-libldap-dev_2.6.10+dfsg-1+b2_amd64.deb ... Unpacking libldap-dev:amd64 (2.6.10+dfsg-1+b2) ... Selecting previously unselected package libpkgconf7:amd64. Preparing to unpack .../62-libpkgconf7_2.5.1-4_amd64.deb ... Unpacking libpkgconf7:amd64 (2.5.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../63-pkgconf-bin_2.5.1-4_amd64.deb ... Unpacking pkgconf-bin (2.5.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../64-pkgconf_2.5.1-4_amd64.deb ... Unpacking pkgconf:amd64 (2.5.1-4) ... Selecting previously unselected package libnghttp2-dev:amd64. Preparing to unpack .../65-libnghttp2-dev_1.69.0-1_amd64.deb ... Unpacking libnghttp2-dev:amd64 (1.69.0-1) ... Selecting previously unselected package libnghttp3-dev:amd64. Preparing to unpack .../66-libnghttp3-dev_1.15.0-1_amd64.deb ... Unpacking libnghttp3-dev:amd64 (1.15.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:amd64. Preparing to unpack .../67-libngtcp2-crypto-gnutls-dev_1.22.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Selecting previously unselected package libngtcp2-dev:amd64. Preparing to unpack .../68-libngtcp2-dev_1.22.1-1_amd64.deb ... Unpacking libngtcp2-dev:amd64 (1.22.1-1) ... Selecting previously unselected package libpsl-dev:amd64. Preparing to unpack .../69-libpsl-dev_0.21.5-1_amd64.deb ... Unpacking libpsl-dev:amd64 (0.21.5-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../70-librtmp1_2.6-1_amd64.deb ... Unpacking librtmp1:amd64 (2.6-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../71-zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Selecting previously unselected package librtmp-dev:amd64. Preparing to unpack .../72-librtmp-dev_2.6-1_amd64.deb ... Unpacking librtmp-dev:amd64 (2.6-1) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../73-libssl-dev_3.6.2-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.6.2-1) ... Selecting previously unselected package libssh2-1-dev:amd64. Preparing to unpack .../74-libssh2-1-dev_1.11.1-2_amd64.deb ... Unpacking libssh2-1-dev:amd64 (1.11.1-2) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../75-libzstd-dev_1.5.7+dfsg-3+b1_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.7+dfsg-3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../76-libcurl4-gnutls-dev_8.20.0~rc3-1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.20.0~rc3-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../77-libdeflate0_1.23-2+b2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2+b2) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../78-libdeflate-dev_1.23-2+b2_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.23-2+b2) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../79-libhtscodecs2_1.6.6-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.6-1) ... Selecting previously unselected package libhtscodecs-dev:amd64. Preparing to unpack .../80-libhtscodecs-dev_1.6.6-1_amd64.deb ... Unpacking libhtscodecs-dev:amd64 (1.6.6-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../81-liblzma-dev_5.8.3-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.3-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../82-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.6-1) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up libkeyutils1:amd64 (1.6.3-6+b2) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-3+b1) ... Setting up bsdextrautils (2.42-5) ... Setting up libmagic-mgc (1:5.46-5+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.2+dfsg-0.1) ... Setting up libdebhelper-perl (13.31) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.46-5+b2) ... Setting up libpsl5t64:amd64 (0.21.5-1) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libdeflate0:amd64 (1.23-2+b2) ... Setting up gettext-base (0.23.2-2) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up file (1:5.46-5+b2) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up libpsl-dev:amd64 (0.21.5-1) ... Setting up libkrb5support0:amd64 (1.22.1-2+b1) ... Setting up libhtscodecs-dev:amd64 (1.6.6-1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.24.2-1+b1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libgnutls-dane0t64:amd64 (3.8.12-3) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b2) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libssl-dev:amd64 (3.6.2-1) ... Setting up autopoint (0.23.2-2) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-2+b1) ... Setting up libidn2-dev:amd64 (2.3.8-4+b1) ... Setting up autoconf (2.72-6) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b1) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-2+b1) ... Setting up libssh2-1t64:amd64 (1.11.1-2) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2+b2) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libp11-kit-dev:amd64 (0.26.2-2) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.2-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2+b1) ... Setting up libssh2-1-dev:amd64 (1.11.1-2) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.24.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.12-3) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up po-debconf (1.0.22) ... Setting up libcurl3t64-gnutls:amd64 (8.20.0~rc3-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.22.1-2+b1) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-2+b1) ... Setting up libkdb5-10t64:amd64 (1.22.1-2+b1) ... Setting up debhelper (13.31) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-2+b1) ... Setting up krb5-multidev:amd64 (1.22.1-2+b1) ... Setting up libkrb5-dev:amd64 (1.22.1-2+b1) ... Setting up libcurl4-gnutls-dev:amd64 (8.20.0~rc3-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-15) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 26 Apr 2026 23:32:55 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sun, 26 Apr 2026 23:32:55 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.18.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.18.5-1 (2026-01-16) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-14_14.3.0-14 g++-15_15.2.0-17 gcc-14_14.3.0-14 gcc-15_15.2.0-17 libc6-dev_2.42-15 libstdc++-14-dev_14.3.0-14 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260425-1 linux-libc-dev_6.19.14-1 Package versions: adduser_3.155 apt_3.2.0 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1+nmu1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-3 binutils-common_2.46-3 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.42-5 bsdutils_1:2.42-5 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-14_14.3.0-14 cpp-14-x86-64-linux-gnu_14.3.0-14 cpp-15_15.2.0-17 cpp-15-x86-64-linux-gnu_15.2.0-17 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dirmngr_2.4.9-4 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.46-5+b2 findutils_4.10.0-3 g++_4:15.2.0-5+b1 g++-14_14.3.0-14 g++-14-x86-64-linux-gnu_14.3.0-14 g++-15_15.2.0-17 g++-15-x86-64-linux-gnu_15.2.0-17 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-14_14.3.0-14 gcc-14-base_14.3.0-14 gcc-14-x86-64-linux-gnu_14.3.0-14 gcc-15_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-x86-64-linux-gnu_15.2.0-17 gcc-16-base_16-20260425-1 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_0.23.2-2 gettext-base_0.23.2-2 gnupg_2.4.9-4 gnupg-l10n_2.4.9-4 gpg_2.4.9-4 gpg-agent_2.4.9-4 gpgconf_2.4.9-4 gpgsm_2.4.9-4 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-2+b1 libacl1_2.3.2-3 libapt-pkg7.0_3.2.0 libarchive-zip-perl_1.68-1 libasan8_16-20260425-1 libassuan9_3.0.2-2+b2 libatomic1_16-20260425-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.42-5 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b2 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-15 libc-dev-bin_2.42-15 libc-gconv-modules-extra_2.42-15 libc-l10n_2.42-15 libc6_2.42-15 libc6-dev_2.42-15 libcap-ng0_0.9.3-1 libcap2_1:2.78-1 libcc1-0_16-20260425-1 libcom-err2_1.47.4-1 libcrypt-dev_1:4.5.1-1+b1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl3t64-gnutls_8.20.0~rc3-1 libcurl4-gnutls-dev_8.20.0~rc3-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.282+b3 libdebhelper-perl_13.31 libdeflate-dev_1.23-2+b2 libdeflate0_1.23-2+b2 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-14-dev_14.3.0-14 libgcc-15-dev_15.2.0-17 libgcc-s1_16-20260425-1 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.12-3 libgnutls28-dev_3.8.12-3 libgnutls30t64_3.8.12-3 libgomp1_16-20260425-1 libgpg-error0_1.59-4 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2+b1 libgssrpc4t64_1.22.1-2+b1 libhogweed6t64_3.10.2-1+b1 libhtscodecs-dev_1.6.6-1 libhtscodecs2_1.6.6-1 libhwasan0_16-20260425-1 libidn2-0_2.3.8-4+b1 libidn2-dev_2.3.8-4+b1 libisl23_0.27-2 libitm1_16-20260425-1 libjansson4_2.14-2+b4 libk5crypto3_1.22.1-2+b1 libkadm5clnt-mit12_1.22.1-2+b1 libkadm5srv-mit12_1.22.1-2+b1 libkdb5-10t64_1.22.1-2+b1 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-2+b1 libkrb5-dev_1.22.1-2+b1 libkrb5support0_1.22.1-2+b1 libksba8_1.6.8-2 liblastlog2-2_2.42-5 libldap-dev_2.6.10+dfsg-1+b2 libldap2_2.6.10+dfsg-1+b2 liblsan0_16-20260425-1 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.46-5+b2 libmagic1t64_1:5.46-5+b2 libmd0_1.1.0-2+b2 libmount1_2.42-5 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b1 libp11-kit-dev_0.26.2-2 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7+b2 libperl5.42_5.42.2-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.21.5-1 libpsl5t64_0.21.5-1 libquadmath0_16-20260425-1 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsemanage-common_3.10-1 libsemanage2_3.10-1 libsepol2_3.10-1 libsframe2_2.45.50.20251209-1+b1 libsframe3_2.46-3 libsmartcols1_2.42-5 libsqlite3-0_3.46.1-9+b1 libssh2-1-dev_1.11.1-2 libssh2-1t64_1.11.1-2 libssl-dev_3.6.2-1 libssl3t64_3.6.2-1 libstdc++-14-dev_14.3.0-14 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260425-1 libsystemd0_260.1-1 libtasn1-6_4.21.0-2 libtasn1-6-dev_4.21.0-2 libtinfo6_6.6+20251231-1 libtool_2.5.4-11 libtsan2_16-20260425-1 libubsan1_16-20260425-1 libuchardet0_0.0.8-2+b1 libudev1_260.1-1 libunbound8_1.24.2-1+b1 libunistring5_1.4.2-1 libuuid1_2.42-5 libxml2-16_2.15.2+dfsg-0.1 libxxhash0_0.8.3-2+b1 libzstd-dev_1.5.7+dfsg-3+b1 libzstd1_1.5.7+dfsg-3+b1 linux-libc-dev_6.19.14-1 locales-all_2.42-15 login.defs_1:4.19.3-2 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.2-1 passwd_1:4.19.3-2 patch_2.8-2 perl_5.42.2-1 perl-base_5.42.2-1 perl-modules-5.40_5.40.1-7 perl-modules-5.42_5.42.2-1 pinentry-curses_1.3.2-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.3.0-5+b1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 util-linux_2.42-5 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 26 Apr 2026 23:32:55 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htslib Binary: libhts3t64, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.22.1+ds2-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3t64 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: ce3c0511527a8bc8a3327cf6aaa38b28ec271e0c 1593472 htslib_1.22.1+ds2.orig.tar.bz2 47a81c0b05b2700d0660b453fa5ddb3ded7e5cb4 22004 htslib_1.22.1+ds2-1.debian.tar.xz Checksums-Sha256: 911a26eb37943726c5f616bd8044144dbdcc0c127e8770f6b82ed0627f3dbd80 1593472 htslib_1.22.1+ds2.orig.tar.bz2 e97c8951ce5ff4d80c7dc3f2c0b8a4b73ddf18f7d219f2b15aaf104af4b28018 22004 htslib_1.22.1+ds2-1.debian.tar.xz Files: 435ce1c1b723732c43d0925889e2d3d4 1593472 htslib_1.22.1+ds2.orig.tar.bz2 ded83a10f428ad5a72615e496d651719 22004 htslib_1.22.1+ds2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmi5imkSHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+biGAYP/1aC/QvynNdNcVe3ikuDnnZFhSiQbj4k 3m39CS5oS5ZjJuNW2GaZvEZHcPWoUjb7bwjbkh9oee9D2fK8JezxAe5ILnB0PA6K BMfn9mzDcrLiJSSUk++wUzog79XIT2YW63l1wSc0MAtaJyNUJZomDjcvOCoQX/j0 7Rz77h6TkkO60isA7e30AKToL+u0SeNzD8MkiJDJbE0NxhxGgd/zhM8w+RlK3VnM MbpjepUwV2GxD0IIEt6hPgF6cbZWR4guBQPClrvb7ZYpn5uIf19vE9xMyDw6mRB8 Bz892I2NyYsotOtsa+i7qy/SNKMtXdYB2pCglpJPOcqsx6DFUqsC4QeO2K14YiDA roBlRukKPfrOFyc+uXvXInyW4BiROux7fV7EBhz8msfrN9MQX7K8rJzLt7hB+gCt +CqZEepEOldbdMCRGpD/YBD01BvtdP87MJeqkeoqVbpz5+yuG3TYtalYQmTut6ky FmFXCUjsb5TySqRMB09sOUyqd+raWjjLyU/J/PeA5Jy1VrctWvGkeTiYCQjhroG2 f+lZxtxqBholSfwMXGTwc4ayDDUM3Rj3eudCEjeB2l6qVsOESLTZfGwtZKNEbg5g vEXGVqxpUozr3FvisF3Lk7HS81k1r9juqr6Ss5S3cjh8WFrX1wskJIcu0y8MicwV tCS6yVoks8/2 =DUBu -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./htslib_1.22.1+ds2-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./htslib_1.22.1+ds2-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting htslib in /build/htslib-BlqyQO/htslib-1.22.1+ds2 dpkg-source: info: unpacking htslib_1.22.1+ds2.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.22.1+ds2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 26 Apr 2026 23:32:56 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.22.1+ds2-1 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.22.1+ds2-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/htslib-BlqyQO/htslib-1.22.1+ds2 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-3409e65f-de56-4657-a096-861caf805e27 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.22.1+ds2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean dh_auto_clean make -j2 distclean make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \ test/longrefs/*.tmp.* test/ref_cache/*.tmp.* test/tabix/*.tmp.* \ test/bgzf_boundaries/*.tmp.* test/*/FAIL* \ header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f ref_cache/*.o rm -f libhts.a annot-tsv bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_faidx test/test_kfunc test/test_khash test/test_kstring test/test_mod test/test_nibbles test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' rm -rf test_backup/ make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3t64/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) dpkg-source -Zxz -b . dpkg-source: info: using options from /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building htslib using existing ../htslib_1.22.1+ds2.orig.tar.bz2 dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building htslib in ../htslib_1.22.1+ds2-1.debian.tar.xz dpkg-source: info: building htslib in ../htslib_1.22.1+ds2-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i -v autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: configure.ac: not using Automake autoreconf: './config.sub' is created autoreconf: './config.guess' is created autoreconf: Leaving directory '.' find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/x86_64-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/x86_64-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... yes checking whether __cpuid_count is declared... yes checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt checking C compiler flags needed for avx2... -mavx2 -mpopcnt checking C compiler flags needed for avx512f... -mavx512f -mpopcnt checking for working __builtin_cpu_supports("ssse3")... yes checking for working __attribute__((target("ssse3")))... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for getpagesize... yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for CMSG_LEN... yes checking for epoll... yes (edge triggered) checking for sendfile... yes, Linux-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... yes checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... yes checking whether the compiler accepts -Wstrict-aliasing... yes checking whether the compiler accepts -fstack-clash-protection... yes checking whether the compiler accepts -fstack-protector-strong... yes checking whether the compiler accepts -fcf-protection=full... yes checking whether the compiler accepts -mbranch-protection=standard... no checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_external.mk to htscodecs.mk make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu make -j2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" CPPFLAGS="-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.22.1"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o simd.o simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o simd.pico simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o annot-tsv.o annot-tsv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_khash.o test/test_khash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_nibbles.o test/test_nibbles.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/http_parser.o ref_cache/http_parser.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/listener.o ref_cache/listener.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/log_files.o ref_cache/log_files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/main.o ref_cache/main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/misc.o ref_cache/misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/ping.o ref_cache/ping.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/ref_files.o ref_cache/ref_files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/request_handler.o ref_cache/request_handler.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/server.o ref_cache/server.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/transaction.o ref_cache/transaction.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/upstream.o ref_cache/upstream.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl ln -sf libhts.so libhts.so.3 ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread make[2]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j2 test TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" CPPFLAGS="-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && \ if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ else \ REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ fi bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 14 -x /tmp/ThDuQDCiqn/index.bam.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 0 -x /tmp/ThDuQDCiqn/index.bam.bai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -b /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/ThDuQDCiqn/index.sam.gz.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/ThDuQDCiqn/index.sam.gz.bai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -b /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/ThDuQDCiqn/index.sam.gz.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/ThDuQDCiqn/index.sam.gz.bai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -b /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -C -x /tmp/ThDuQDCiqn/index.cram.crai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.cram .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index /tmp/ThDuQDCiqn/index.cram .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 14 -x /tmp/ThDuQDCiqn/index.bcf.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.vcf > /tmp/ThDuQDCiqn/index.bcf .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.bcf .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/ThDuQDCiqn/index.vcf.gz.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.vcf > /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/ThDuQDCiqn/index.vcf.gz.tbi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.vcf > /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -t /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/tabix /tmp/ThDuQDCiqn/index.vcf.gz##idx##/tmp/ThDuQDCiqn/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 2:2000000-2000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 14 -x /tmp/ThDuQDCiqn/index.bam.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 0 -x /tmp/ThDuQDCiqn/index.bam.bai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -b /tmp/ThDuQDCiqn/index.bam .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/ThDuQDCiqn/index.sam.gz.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/ThDuQDCiqn/index.sam.gz.bai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -b /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/ThDuQDCiqn/index.sam.gz.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/ThDuQDCiqn/index.sam.gz.bai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -b /tmp/ThDuQDCiqn/index.sam.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -C -x /tmp/ThDuQDCiqn/index.cram.crai /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.sam > /tmp/ThDuQDCiqn/index.cram .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index /tmp/ThDuQDCiqn/index.cram .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 14 -x /tmp/ThDuQDCiqn/index.bcf.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.vcf > /tmp/ThDuQDCiqn/index.bcf .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.bcf .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/ThDuQDCiqn/index.vcf.gz.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.vcf > /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/ThDuQDCiqn/index.vcf.gz.tbi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/index.vcf > /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -t /tmp/ThDuQDCiqn/index.vcf.gz .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/tabix /tmp/ThDuQDCiqn/index.vcf.gz##idx##/tmp/ThDuQDCiqn/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /tmp/ThDuQDCiqn/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#bounds_er.tmp.cram.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-vcf-api /tmp/ThDuQDCiqn/test-vcf-api.bcf .. ok test_bcf2vcf: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-vcf-sweep /tmp/ThDuQDCiqn/test-vcf-api.bcf .. ok test_vcf_various: /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile -ch /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile -c /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/formatcols.vcf .. ok test_vcf_various: /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile -c /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/noroundtrip.vcf .. ok test_vcf_various: /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile -c /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/formatmissing.vcf .. ok test_vcf_various: /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile -c /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile -c /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/vcf44_1.vcf .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 74452500 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 34270147 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 11108528 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 42233895 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 8111117 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 85644070 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 49879942 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 47881429 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 69081244 .. ok test-bcf-sr: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/ThDuQDCiqn -s 83459376 .. ok test_bcf_sr_no_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.b.vcf /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/ThDuQDCiqn/no_index_1.err .. ok test_bcf_sr_no_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/ThDuQDCiqn/no_index_2.out 2> /tmp/ThDuQDCiqn/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/ThDuQDCiqn/no_index_3.out 2> /tmp/ThDuQDCiqn/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.rec_order.vcf /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf > /tmp/ThDuQDCiqn/no_index_4.out 2> /tmp/ThDuQDCiqn/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -b -p /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf -x /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf.csi /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_1.out.vcf -r '1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_2.out.vcf -r '1:1-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_4.out.vcf -r '1:1-1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_5.out.vcf -r '{1:1}' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_14.out.vcf -t '1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_15.out.vcf -t '1:1-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_17.out.vcf -t '1:1-1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_18.out.vcf -t '{1:1}' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/ThDuQDCiqn/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/ThDuQDCiqn/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok .. ok test_command: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf-translate - .. ok test_convert_padded_header: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/ThDuQDCiqn/headernul0.bam .. ok test_convert_padded_header: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/ThDuQDCiqn/headernul1.bam .. ok test_convert_padded_header: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/ThDuQDCiqn/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/htslib-BlqyQO/htslib-1.22.1+ds2/bgzip -I /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bgziptest.txt.tmp.gz.gzi -c -g /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/bgziptest.txt .. ok test-logging: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/htslib-BlqyQO/htslib-1.22.1+ds2 /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/with-shlib.sh /build/htslib-BlqyQO/htslib-1.22.1+ds2/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn01.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -a -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn01.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -a -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -e -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn01.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -e -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -r -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02-r.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -a -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02_exp.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn02_exp-a.sam -o - .. ok test_realn: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn03.fa -e -i /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -f smpl -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -x -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -x -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -x -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -x -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -x -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -m smpl -x -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -s /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt | /build/htslib-BlqyQO/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -t /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok ref-cache: ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam .. ok Number of tests: total .. 352 passed .. 352 failed .. 0 make[2]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' rm -fr -- /tmp/dh-xdg-rundir-94SHIGjn make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3t64/ debian/libhts3t64/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/htslib-test/ debian/htslib-test/ debian/.debhelper/generated/tabix/ debian/tabix/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/htslib-BlqyQO/htslib-1.22.1+ds2/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/htslib-BlqyQO/htslib-1.22.1\+ds2/debian/tmp make -j2 install DESTDIR=/build/htslib-BlqyQO/htslib-1.22.1\+ds2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-BlqyQO/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" CPPFLAGS="-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' mkdir -p -m 755 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/bin /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/include /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/include/htslib /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man5 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man7 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig if test -n "/usr/lib/x86_64-linux-gnu/htslib"; then mkdir -p -m 755 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.22.1#g' htslib.pc.tmp > /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc chmod 644 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.22.1 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.22.1 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ install -p -m 644 ref_cache/ref-cache.1 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 ; \ fi install -p -m 644 faidx.5 sam.5 vcf.5 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_install install -m0755 -d debian/libhts3t64/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/htslib debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 debian/libhts3t64/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts3t64/usr/share/man/man5 cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man5/ install -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -m0755 -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -m0755 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./annot-tsv.c ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./builddir_vars.mk.in ./config.h.in ./config.mk.in ./configure.ac ./errmod.c ./faidx.c ./fuzz_settings.h ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_expr.c ./hts_internal.h ./hts_os.c ./hts_time_funcs.h ./htscodecs.mk ./htscodecs_bundled.mk ./htscodecs_external.mk ./htsfile.c ./htslib.mk ./htslib.pc.in ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./sam_mods.c ./simd.c ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.sh debian/htslib-test/usr/share/htslib-test/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/m4 cp --reflink=auto -a ./m4/hts_check_compile_flags_needed.m4 ./m4/hts_hide_dynamic_syms.m4 ./m4/hts_prog_cc_warnings.m4 ./m4/pkg.m4 debian/htslib-test/usr/share/htslib-test/m4/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/ref_cache cp --reflink=auto -a ./ref_cache/cmsg_wrap.c ./ref_cache/cmsg_wrap.h ./ref_cache/http_parser.c ./ref_cache/http_parser.h ./ref_cache/listener.c ./ref_cache/listener.h ./ref_cache/log_files.c ./ref_cache/log_files.h ./ref_cache/main.c ./ref_cache/misc.c ./ref_cache/misc.h ./ref_cache/options.h ./ref_cache/ping.c ./ref_cache/ping.h ./ref_cache/poll_wrap.h ./ref_cache/poll_wrap_epoll.c ./ref_cache/poll_wrap_poll.c ./ref_cache/ref_files.c ./ref_cache/ref_files.h ./ref_cache/request_handler.c ./ref_cache/request_handler.h ./ref_cache/sendfile_wrap.c ./ref_cache/sendfile_wrap.h ./ref_cache/server.c ./ref_cache/server.h ./ref_cache/transaction.c ./ref_cache/transaction.h ./ref_cache/types.h ./ref_cache/upstream.c ./ref_cache/upstream.h debian/htslib-test/usr/share/htslib-test/ref_cache/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/annot-tsv ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/base_mods ./test/bcf-sr ./test/bgzf_boundaries ./test/bgziptest.txt ./test/bgziptest.txt.gz ./test/bgziptest.txt.gz.gzi ./test/c1\#bounds.sam ./test/c1\#clip.sam ./test/c1\#noseq.sam ./test/c1\#pad1.sam ./test/c1\#pad2.sam ./test/c1\#pad3.sam ./test/c1\#unknown.sam ./test/c1.fa ./test/c1.fa.fai ./test/c2\#pad.sam ./test/c2.fa ./test/c2.fa.fai ./test/ce\#1.sam ./test/ce\#1000.sam ./test/ce\#2.sam ./test/ce\#5.sam ./test/ce\#5b.sam ./test/ce\#5b_java.cram ./test/ce\#large_seq.sam ./test/ce\#supp.sam ./test/ce\#tag_depadded.sam ./test/ce\#tag_padded.sam ./test/ce\#unmap.sam ./test/ce\#unmap1.sam ./test/ce\#unmap2.sam ./test/ce.fa ./test/ce.fa.fai ./test/colons.bam ./test/colons.bam.bai ./test/compare_sam.pl ./test/cross_validate.sh ./test/emptyfile ./test/faidx ./test/fastq ./test/fastqs_README.txt ./test/fieldarith.c ./test/fieldarith.sam ./test/formatcols.vcf ./test/formatmissing-out.vcf ./test/formatmissing.vcf ./test/fuzz ./test/header_syms.pl ./test/hfile.c ./test/hts_endian.c ./test/index.bam.bai ./test/index.bam.csi ./test/index.bcf.csi ./test/index.cram.crai ./test/index.sam ./test/index.sam.gz.bai ./test/index.sam.gz.csi ./test/index.vcf ./test/index.vcf.gz.csi ./test/index.vcf.gz.tbi ./test/index2.sam ./test/index_dos.sam ./test/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/modhdr.expected.vcf ./test/modhdr.vcf.gz ./test/modhdr.vcf.gz.csi ./test/mpileup ./test/no_hdr_sq_1.bam ./test/no_hdr_sq_1.bam.csi ./test/no_hdr_sq_1.expected.sam ./test/noroundtrip-out.vcf ./test/noroundtrip.vcf ./test/pileup.c ./test/pileup_mod.c ./test/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./test/range.out2 ./test/realn01.fa ./test/realn01.fa.fai ./test/realn01.sam ./test/realn01_exp-a.sam ./test/realn01_exp-e.sam ./test/realn01_exp.sam ./test/realn02-r.sam ./test/realn02.fa ./test/realn02.fa.fai ./test/realn02.sam ./test/realn02_exp-a.sam ./test/realn02_exp-e.sam ./test/realn02_exp.sam ./test/realn03.fa ./test/realn03.fa.fai ./test/realn03.sam ./test/realn03_exp.sam ./test/ref_cache ./test/sam.c ./test/sam_filter ./test/simple_test_driver.sh ./test/tabix ./test/tabix.out ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-bcf_set_variant_type.c ./test/test-logging.pl ./test/test-parse-reg.c ./test/test-regidx.c ./test/test-vcf-api.c ./test/test-vcf-api.out ./test/test-vcf-hdr-in.vcf ./test/test-vcf-hdr.out ./test/test-vcf-sweep.c ./test/test-vcf-sweep.out ./test/test.pl ./test/test_bgzf.c ./test/test_expr.c ./test/test_faidx.c ./test/test_index.c ./test/test_introspection.c ./test/test_kfunc.c ./test/test_khash.c ./test/test_kstring.c ./test/test_mod.c ./test/test_nibbles.c ./test/test_realn.c ./test/test_str2int.c ./test/test_time_funcs.c ./test/test_view.c ./test/thrash_threads1.c ./test/thrash_threads2.c ./test/thrash_threads3.c ./test/thrash_threads4.c ./test/thrash_threads5.c ./test/thrash_threads6.c ./test/thrash_threads7.c ./test/thread_pool.md ./test/usepublic.cpp ./test/vcf44_1.expected ./test/vcf44_1.vcf ./test/vcf_meta_meta.vcf ./test/with-shlib.sh ./test/xx\#MD.sam ./test/xx\#MD2.sam ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#u.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules execute_after_dh_install-indep make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_installdocs install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/copyright debian/libhts3t64/usr/share/doc/libhts3t64/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so: No such file or directory make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_installchangelogs NEWS install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/.debhelper/generated/libhts3t64/dh_installchangelogs.dch.trimmed debian/libhts3t64/usr/share/doc/libhts3t64/changelog.Debian install -p -m0644 NEWS debian/libhts3t64/usr/share/doc/libhts3t64/changelog install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_installman install -m0755 -d debian/libhts3t64/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 debian/tabix/usr/share/man/man1/tabix.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 debian/tabix/usr/share/man/man1/tabix.1 mv debian/libhts3t64/usr/share/man/man5/faidx.5.dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 mv debian/libhts3t64/usr/share/man/man5/sam.5.dh-new debian/libhts3t64/usr/share/man/man5/sam.5 mv debian/libhts3t64/usr/share/man/man5/vcf.5.dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 mv debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 dh_lintian install -m0755 -d debian/libhts-dev/usr/share/lintian/overrides install -p -m0644 debian/libhts-dev.lintian-overrides debian/libhts-dev/usr/share/lintian/overrides/libhts-dev install -m0755 -d debian/htslib-test/usr/share/lintian/overrides install -p -m0644 debian/htslib-test.lintian-overrides debian/htslib-test/usr/share/lintian/overrides/htslib-test dh_perl mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 ln -s libhts.so.1.22.1 debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -s libhts.so.1.22.1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/htslib-test/usr/share/htslib-test/htscodecs.mk ln -s htscodecs_external.mk debian/htslib-test/usr/share/htslib-test/htscodecs.mk install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism Using 1756986990 as canonical time Normalizing debian/htslib-test/usr/share/htslib-test/test/modhdr.vcf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/htslib-test/usr/share/htslib-test/test/bgziptest.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/libhts3t64 cd debian/htslib-test chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian chmod a-x usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 cd '/build/htslib-BlqyQO/htslib-1.22.1+ds2' cd debian/tabix cd '/build/htslib-BlqyQO/htslib-1.22.1+ds2' cd debian/libhts-dev chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 cd '/build/htslib-BlqyQO/htslib-1.22.1+ds2' cd '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_fixperms find debian/libhts3t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libhts-dev/usr/include debian/libhts-dev/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' debian/rules execute_before_dh_missing make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_missing dh_dwz -a install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1: DWARF compression not beneficial - old size 977833 new size 1001399 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug debian/rules override_dh_strip make[1]: Entering directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/1b objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/1b/470e55db2986890ed6347463a1936764d1fdd3.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0c/883c14ebf37faccea93566ac45dd3768872613.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0c/883c14ebf37faccea93566ac45dd3768872613.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/1b/470e55db2986890ed6347463a1936764d1fdd3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/1b/470e55db2986890ed6347463a1936764d1fdd3.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0c/883c14ebf37faccea93566ac45dd3768872613.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/50 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/50/61fb73c04dfde3d859739c02b422288e739274.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/41 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/41/d10903ae44bd6d82cb50c485c48a7725860a5a.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/50/61fb73c04dfde3d859739c02b422288e739274.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/50/61fb73c04dfde3d859739c02b422288e739274.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/2b objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/2b/71e863c96319fcbd8537ef9e801ba3e91143fe.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/2b/71e863c96319fcbd8537ef9e801ba3e91143fe.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/2b/71e863c96319fcbd8537ef9e801ba3e91143fe.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/bd/84982550d7999c3c2e07fcb0ee1de58f7db0a7.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/bd/84982550d7999c3c2e07fcb0ee1de58f7db0a7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/bd/84982550d7999c3c2e07fcb0ee1de58f7db0a7.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/b4 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/b4/5e87a3d5bfbe62ce58383a2c423f1848bc2ee4.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/b4/5e87a3d5bfbe62ce58383a2c423f1848bc2ee4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/b4/5e87a3d5bfbe62ce58383a2c423f1848bc2ee4.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3t64/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc ln -s libhts3t64 debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc/libhts3t64-dbgsym install -m0755 -d debian/.debhelper/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/41/d10903ae44bd6d82cb50c485c48a7725860a5a.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/41/d10903ae44bd6d82cb50c485c48a7725860a5a.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d8 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d8/9db76efced011f372603cc41d9805728bfbfaf.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d8/9db76efced011f372603cc41d9805728bfbfaf.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d8/9db76efced011f372603cc41d9805728bfbfaf.debug debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/build/htslib-BlqyQO/htslib-1.22.1+ds2' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.22.1+ds2)" >> debian/libhts3t64/DEBIAN/shlibs chmod 0644 -- debian/libhts3t64/DEBIAN/shlibs dpkg-gensymbols -plibhts3t64 -Idebian/libhts3t64.symbols -Pdebian/libhts3t64 -edebian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers mv debian/libhts3t64.substvars.new debian/libhts3t64.substvars rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so install -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile dh_installdeb install -m0755 -d debian/libhts3t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3t64/triggers debian/libhts3t64/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol install -m0755 -d debian/libhts3t64/DEBIAN echo misc:Depends= >> debian/libhts3t64.substvars echo misc:Pre-Depends= >> debian/libhts3t64.substvars install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/.debhelper/libhts3t64/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libhts3t64-dbgsym -DDepends="libhts3t64 (= \${binary:Version})" -DDescription="debug symbols for libhts3t64" -DBuild-Ids="1b470e55db2986890ed6347463a1936764d1fdd3 2b71e863c96319fcbd8537ef9e801ba3e91143fe 5061fb73c04dfde3d859739c02b422288e739274 b45e87a3d5bfbe62ce58383a2c423f1848bc2ee4 bd84982550d7999c3c2e07fcb0ee1de58f7db0a7" -DSection=debug -DMulti-Arch=same -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN echo misc:Depends= >> debian/htslib-test.substvars echo misc:Pre-Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -cdebian/control -Pdebian/htslib-test chmod 0644 -- debian/htslib-test/DEBIAN/control install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=tabix-dbgsym -DDepends="tabix (= \${binary:Version})" -DDescription="debug symbols for tabix" -DBuild-Ids="0c883c14ebf37faccea93566ac45dd3768872613 41d10903ae44bd6d82cb50c485c48a7725860a5a d89db76efced011f372603cc41d9805728bfbfaf" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/tabix chmod 0644 -- debian/libhts3t64/DEBIAN/control install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -cdebian/control -Pdebian/libhts-dev chmod 0644 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts-dev/DEBIAN/control dh_md5sums install -m0755 -d debian/libhts3t64/DEBIAN cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/htslib-test/DEBIAN cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums install -m0755 -d debian/libhts-dev/DEBIAN cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums install -m0755 -d debian/tabix/DEBIAN cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.22.1+ds2-1_all.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'tabix' in '../tabix_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.22.1+ds2-1_amd64.deb'. dpkg-genbuildinfo -O../htslib_1.22.1+ds2-1_amd64.buildinfo dpkg-genchanges -O../htslib_1.22.1+ds2-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from /build/htslib-BlqyQO/htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2026-04-26T23:35:04Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 26 Apr 2026 23:35:04 +0000 | +------------------------------------------------------------------------------+ htslib_1.22.1+ds2-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Thu, 04 Sep 2025 13:56:30 +0200 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: source all amd64 Version: 1.22.1+ds2-1 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: htslib-test - Test data for HTSlib libhts-dev - development files for the HTSlib libhts3t64 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.22.1+ds2-1) unstable; urgency=medium . * Properly clean the upstream release tarball. * Don't ship architecture-specific files in htslib-test; regenerate them at test-time using autoconf. * d/libhts3t64.symbols: add new symbols for the latest release. Checksums-Sha1: f6c6fb11ecdb96e7e941fe91c7c9bf9db3f05c98 1565 htslib_1.22.1+ds2-1.dsc ce3c0511527a8bc8a3327cf6aaa38b28ec271e0c 1593472 htslib_1.22.1+ds2.orig.tar.bz2 6bc3b84150356b5d0f8cb8881401906ef4984238 22000 htslib_1.22.1+ds2-1.debian.tar.xz 181ecff346053624f8d315683f128bf1381f3feb 1223980 htslib-test_1.22.1+ds2-1_all.deb 48435c331062f3a7533096ed5a880a0cbbf25aba 8482 htslib_1.22.1+ds2-1_amd64.buildinfo 22cdf604d40e9515c0e5928885e6f982876b2e2e 1784944 libhts-dev_1.22.1+ds2-1_amd64.deb bb01332143f36f334422e43fac97374278ccbe0b 1351128 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 0ec3a93fa91a4a264517fa35c7a11ad6860b276a 475172 libhts3t64_1.22.1+ds2-1_amd64.deb 70912256f87255dba847e94fc3880f4db541dd5a 3127976 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 92b46589ccaea2c7c56f7ff5434c228bc815e48b 506944 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha256: 8a807efc88a64c375869d3efe66db661e2c4b6ccf9f444eecf5d9d222791d396 1565 htslib_1.22.1+ds2-1.dsc 911a26eb37943726c5f616bd8044144dbdcc0c127e8770f6b82ed0627f3dbd80 1593472 htslib_1.22.1+ds2.orig.tar.bz2 12144122391e1e9d992a6c5f3f5017c432c02210555ceb84ff00f09fafec6052 22000 htslib_1.22.1+ds2-1.debian.tar.xz cb7960f05df9ed0ec6009f2244aca7de2bc80eec5fc1f0e42bd6d2fe91b929d2 1223980 htslib-test_1.22.1+ds2-1_all.deb 631f845fafed23d8f79621aa04589926350c011df7d141ae528303796bf30233 8482 htslib_1.22.1+ds2-1_amd64.buildinfo 0b0ec600b5a7439262c6ae9eee30441d66828e1e36fe5ee2e01e564552961559 1784944 libhts-dev_1.22.1+ds2-1_amd64.deb 94cfd72a1016a453ee5fb6136e94ff1d0ba3a3228fb8d09929945ee5cc03c4e1 1351128 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 704de0901223444ebd3a941676ce8b1fdba38373a01da65de6f567b12c5692ff 475172 libhts3t64_1.22.1+ds2-1_amd64.deb f026bc52aa7870219ae746cb70415a07d6676a937547ea6b90d34c854ad4fbb2 3127976 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 670981a56e7db2abee77dca8b8f32e6abc45aed5aec4b16037d69383095c4e3f 506944 tabix_1.22.1+ds2-1_amd64.deb Files: 36fd984b46f288559a8d5f1624583e36 1565 science optional htslib_1.22.1+ds2-1.dsc 435ce1c1b723732c43d0925889e2d3d4 1593472 science optional htslib_1.22.1+ds2.orig.tar.bz2 54d5a893e02c66adc774283e54699cd1 22000 science optional htslib_1.22.1+ds2-1.debian.tar.xz e2eab0dc3d36114a12e8bc1a6171486a 1223980 science optional htslib-test_1.22.1+ds2-1_all.deb a8a5b61c267990731544d200bbe22d87 8482 science optional htslib_1.22.1+ds2-1_amd64.buildinfo 179177b7afbca3bb49d003fe90b11ccb 1784944 libdevel optional libhts-dev_1.22.1+ds2-1_amd64.deb 427efe004f678e8aedddeb15a006c163 1351128 debug optional libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 6d6113b5346fc00507adca8f776f198e 475172 libs optional libhts3t64_1.22.1+ds2-1_amd64.deb 90944413bcadcbf153f5ac953de7240f 3127976 debug optional tabix-dbgsym_1.22.1+ds2-1_amd64.deb 540f80d8aa5200bc717411fbab240b2e 506944 science optional tabix_1.22.1+ds2-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 26 Apr 2026 23:35:04 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: all amd64 source Version: 1.22.1+ds2-1 Checksums-Md5: 36fd984b46f288559a8d5f1624583e36 1565 htslib_1.22.1+ds2-1.dsc e2eab0dc3d36114a12e8bc1a6171486a 1223980 htslib-test_1.22.1+ds2-1_all.deb 179177b7afbca3bb49d003fe90b11ccb 1784944 libhts-dev_1.22.1+ds2-1_amd64.deb 427efe004f678e8aedddeb15a006c163 1351128 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 6d6113b5346fc00507adca8f776f198e 475172 libhts3t64_1.22.1+ds2-1_amd64.deb 90944413bcadcbf153f5ac953de7240f 3127976 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 540f80d8aa5200bc717411fbab240b2e 506944 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha1: f6c6fb11ecdb96e7e941fe91c7c9bf9db3f05c98 1565 htslib_1.22.1+ds2-1.dsc 181ecff346053624f8d315683f128bf1381f3feb 1223980 htslib-test_1.22.1+ds2-1_all.deb 22cdf604d40e9515c0e5928885e6f982876b2e2e 1784944 libhts-dev_1.22.1+ds2-1_amd64.deb bb01332143f36f334422e43fac97374278ccbe0b 1351128 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 0ec3a93fa91a4a264517fa35c7a11ad6860b276a 475172 libhts3t64_1.22.1+ds2-1_amd64.deb 70912256f87255dba847e94fc3880f4db541dd5a 3127976 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 92b46589ccaea2c7c56f7ff5434c228bc815e48b 506944 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha256: 8a807efc88a64c375869d3efe66db661e2c4b6ccf9f444eecf5d9d222791d396 1565 htslib_1.22.1+ds2-1.dsc cb7960f05df9ed0ec6009f2244aca7de2bc80eec5fc1f0e42bd6d2fe91b929d2 1223980 htslib-test_1.22.1+ds2-1_all.deb 0b0ec600b5a7439262c6ae9eee30441d66828e1e36fe5ee2e01e564552961559 1784944 libhts-dev_1.22.1+ds2-1_amd64.deb 94cfd72a1016a453ee5fb6136e94ff1d0ba3a3228fb8d09929945ee5cc03c4e1 1351128 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 704de0901223444ebd3a941676ce8b1fdba38373a01da65de6f567b12c5692ff 475172 libhts3t64_1.22.1+ds2-1_amd64.deb f026bc52aa7870219ae746cb70415a07d6676a937547ea6b90d34c854ad4fbb2 3127976 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 670981a56e7db2abee77dca8b8f32e6abc45aed5aec4b16037d69383095c4e3f 506944 tabix_1.22.1+ds2-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 26 Apr 2026 23:35:04 +0000 Build-Path: /build/htslib-BlqyQO/htslib-1.22.1+ds2 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-6), automake (= 1:1.18.1-4), autopoint (= 0.23.2-2), autotools-dev (= 20240727.1+nmu1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-3), binutils-common (= 2.46-3), binutils-x86-64-linux-gnu (= 2.46-3), bsdextrautils (= 2.42-5), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-14 (= 14.3.0-14), cpp-14-x86-64-linux-gnu (= 14.3.0-14), cpp-15 (= 15.2.0-17), cpp-15-x86-64-linux-gnu (= 15.2.0-17), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.46-5+b2), findutils (= 4.10.0-3), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.2.0-17), g++-15-x86-64-linux-gnu (= 15.2.0-17), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-14 (= 14.3.0-14), gcc-14-base (= 14.3.0-14), gcc-14-x86-64-linux-gnu (= 14.3.0-14), gcc-15 (= 15.2.0-17), gcc-15-base (= 15.2.0-17), gcc-15-x86-64-linux-gnu (= 15.2.0-17), gcc-16-base (= 16-20260425-1), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 0.23.2-2), gettext-base (= 0.23.2-2), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-2+b1), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 16-20260425-1), libatomic1 (= 16-20260425-1), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-3), libblkid1 (= 2.42-5), libbrotli-dev (= 1.2.0-3), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.42-15), libc-dev-bin (= 2.42-15), libc-gconv-modules-extra (= 2.42-15), libc6 (= 2.42-15), libc6-dev (= 2.42-15), libcap-ng0 (= 0.9.3-1), libcc1-0 (= 16-20260425-1), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libcurl3t64-gnutls (= 8.20.0~rc3-1), libcurl4-gnutls-dev (= 8.20.0~rc3-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.282+b3), libdebhelper-perl (= 13.31), libdeflate-dev (= 1.23-2+b2), libdeflate0 (= 1.23-2+b2), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-14-dev (= 14.3.0-14), libgcc-15-dev (= 15.2.0-17), libgcc-s1 (= 16-20260425-1), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.12-3), libgnutls28-dev (= 3.8.12-3), libgnutls30t64 (= 3.8.12-3), libgomp1 (= 16-20260425-1), libgprofng0 (= 2.46-3), libgssapi-krb5-2 (= 1.22.1-2+b1), libgssrpc4t64 (= 1.22.1-2+b1), libhogweed6t64 (= 3.10.2-1+b1), libhtscodecs-dev (= 1.6.6-1), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16-20260425-1), libidn2-0 (= 2.3.8-4+b1), libidn2-dev (= 2.3.8-4+b1), libisl23 (= 0.27-2), libitm1 (= 16-20260425-1), libjansson4 (= 2.14-2+b4), libk5crypto3 (= 1.22.1-2+b1), libkadm5clnt-mit12 (= 1.22.1-2+b1), libkadm5srv-mit12 (= 1.22.1-2+b1), libkdb5-10t64 (= 1.22.1-2+b1), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-2+b1), libkrb5-dev (= 1.22.1-2+b1), libkrb5support0 (= 1.22.1-2+b1), libldap-dev (= 2.6.10+dfsg-1+b2), libldap2 (= 2.6.10+dfsg-1+b2), liblsan0 (= 16-20260425-1), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.46-5+b2), libmagic1t64 (= 1:5.46-5+b2), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.42-5), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp2-dev (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libnghttp3-dev (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls-dev (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libngtcp2-dev (= 1.22.1-1), libp11-kit-dev (= 0.26.2-2), libp11-kit0 (= 0.26.2-2), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpcre2-8-0 (= 10.46-1+b1), libperl5.42 (= 5.42.2-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.21.5-1), libpsl5t64 (= 0.21.5-1), libquadmath0 (= 16-20260425-1), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46-3), libsmartcols1 (= 2.42-5), libssh2-1-dev (= 1.11.1-2), libssh2-1t64 (= 1.11.1-2), libssl-dev (= 3.6.2-1), libssl3t64 (= 3.6.2-1), libstdc++-15-dev (= 15.2.0-17), libstdc++6 (= 16-20260425-1), libsystemd0 (= 260.1-1), libtasn1-6 (= 4.21.0-2), libtasn1-6-dev (= 4.21.0-2), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-11), libtsan2 (= 16-20260425-1), libubsan1 (= 16-20260425-1), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 260.1-1), libunbound8 (= 1.24.2-1+b1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42-5), libxml2-16 (= 2.15.2+dfsg-0.1), libzstd-dev (= 1.5.7+dfsg-3+b1), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.19.14-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.2-1), patch (= 2.8-2), perl (= 5.42.2-1), perl-base (= 5.42.2-1), perl-modules-5.42 (= 5.42.2-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), util-linux (= 2.42-5), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1756986990" +------------------------------------------------------------------------------+ | Package contents Sun, 26 Apr 2026 23:35:04 +0000 | +------------------------------------------------------------------------------+ htslib-test_1.22.1+ds2-1_all.deb -------------------------------- new Debian package, version 2.0. size 1223980 bytes: control archive=12784 bytes. 966 bytes, 23 lines control 40017 bytes, 512 lines md5sums Package: htslib-test Source: htslib Version: 1.22.1+ds2-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 8447 Depends: perl:any Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/samtools/htslib Description: Test data for HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains test files and scripts for the HTSlib. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/htslib-test/ -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/htslib-test/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/htslib-test/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 1463 2025-09-04 10:59 ./usr/share/doc/libhts-dev/run-unit-test drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/ -rw-r--r-- root/root 53693 2025-09-04 11:56 ./usr/share/htslib-test/Makefile -rw-r--r-- root/root 40886 2025-05-01 08:41 ./usr/share/htslib-test/annot-tsv.c -rw-r--r-- root/root 23600 2024-10-21 11:11 ./usr/share/htslib-test/bcf_sr_sort.c -rw-r--r-- root/root 4239 2024-10-21 11:11 ./usr/share/htslib-test/bcf_sr_sort.h -rw-r--r-- root/root 83378 2025-04-10 09:08 ./usr/share/htslib-test/bgzf.c -rw-r--r-- root/root 29931 2025-05-01 08:41 ./usr/share/htslib-test/bgzip.c -rw-r--r-- root/root 2487 2021-04-14 18:34 ./usr/share/htslib-test/builddir_vars.mk.in -rw-r--r-- root/root 6316 2025-09-04 11:56 ./usr/share/htslib-test/config.h.in -rw-r--r-- root/root 3973 2025-04-17 09:02 ./usr/share/htslib-test/config.mk.in -rw-r--r-- root/root 33346 2025-06-26 10:58 ./usr/share/htslib-test/configure.ac drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/cram/ -rw-r--r-- root/root 2420 2020-05-20 23:18 ./usr/share/htslib-test/cram/cram.h -rw-r--r-- root/root 125724 2025-07-01 08:45 ./usr/share/htslib-test/cram/cram_codecs.c -rw-r--r-- root/root 8556 2023-01-20 10:05 ./usr/share/htslib-test/cram/cram_codecs.h -rw-r--r-- root/root 126140 2025-07-02 16:31 ./usr/share/htslib-test/cram/cram_decode.c -rw-r--r-- root/root 4572 2024-03-07 15:14 ./usr/share/htslib-test/cram/cram_decode.h -rw-r--r-- root/root 149978 2024-12-09 09:39 ./usr/share/htslib-test/cram/cram_encode.c -rw-r--r-- root/root 3701 2022-07-19 17:16 ./usr/share/htslib-test/cram/cram_encode.h -rw-r--r-- root/root 33270 2024-09-05 15:21 ./usr/share/htslib-test/cram/cram_external.c -rw-r--r-- root/root 29478 2025-01-23 16:57 ./usr/share/htslib-test/cram/cram_index.c -rw-r--r-- root/root 3866 2020-09-16 09:17 ./usr/share/htslib-test/cram/cram_index.h -rw-r--r-- root/root 177280 2025-07-02 12:04 ./usr/share/htslib-test/cram/cram_io.c -rw-r--r-- root/root 18393 2025-07-02 16:31 ./usr/share/htslib-test/cram/cram_io.h -rw-r--r-- root/root 2911 2021-02-03 10:22 ./usr/share/htslib-test/cram/cram_samtools.h -rw-r--r-- root/root 7055 2023-11-09 17:01 ./usr/share/htslib-test/cram/cram_stats.c -rw-r--r-- root/root 2273 2019-11-19 11:20 ./usr/share/htslib-test/cram/cram_stats.h -rw-r--r-- root/root 29792 2024-10-07 10:47 ./usr/share/htslib-test/cram/cram_structs.h -rw-r--r-- root/root 17233 2020-09-16 09:17 ./usr/share/htslib-test/cram/mFILE.c -rw-r--r-- root/root 3075 2019-11-19 11:20 ./usr/share/htslib-test/cram/mFILE.h -rw-r--r-- root/root 3371 2019-11-19 11:20 ./usr/share/htslib-test/cram/misc.h -rw-r--r-- root/root 14867 2025-05-15 09:10 ./usr/share/htslib-test/cram/open_trace_file.c -rw-r--r-- root/root 5150 2025-05-15 09:10 ./usr/share/htslib-test/cram/open_trace_file.h -rw-r--r-- root/root 6922 2025-09-04 11:56 ./usr/share/htslib-test/cram/os.h -rw-r--r-- root/root 5049 2020-01-07 16:06 ./usr/share/htslib-test/cram/pooled_alloc.c -rw-r--r-- root/root 2185 2019-11-19 11:20 ./usr/share/htslib-test/cram/pooled_alloc.h -rw-r--r-- root/root 4422 2020-09-16 09:17 ./usr/share/htslib-test/cram/string_alloc.c -rw-r--r-- root/root 2356 2019-11-19 11:20 ./usr/share/htslib-test/cram/string_alloc.h -rw-r--r-- root/root 6757 2019-11-19 11:20 ./usr/share/htslib-test/errmod.c -rw-r--r-- root/root 30982 2024-08-15 14:18 ./usr/share/htslib-test/faidx.c -rw-r--r-- root/root 1442 2023-08-07 08:39 ./usr/share/htslib-test/fuzz_settings.h -rw-r--r-- root/root 82309 2025-03-06 09:42 ./usr/share/htslib-test/header.c -rw-r--r-- root/root 10466 2020-01-08 16:24 ./usr/share/htslib-test/header.h -rw-r--r-- root/root 41258 2024-11-14 12:29 ./usr/share/htslib-test/hfile.c -rw-r--r-- root/root 5139 2021-06-22 10:24 ./usr/share/htslib-test/hfile_gcs.c -rw-r--r-- root/root 8112 2022-05-13 15:25 ./usr/share/htslib-test/hfile_internal.h -rw-r--r-- root/root 49245 2025-06-02 09:17 ./usr/share/htslib-test/hfile_libcurl.c -rw-r--r-- root/root 41232 2024-04-05 09:17 ./usr/share/htslib-test/hfile_s3.c -rw-r--r-- root/root 24158 2024-04-29 14:17 ./usr/share/htslib-test/hfile_s3_write.c -rw-r--r-- root/root 169188 2025-02-16 23:20 ./usr/share/htslib-test/hts.c -rw-r--r-- root/root 28501 2024-08-15 14:18 ./usr/share/htslib-test/hts_expr.c -rw-r--r-- root/root 5862 2025-04-10 09:08 ./usr/share/htslib-test/hts_internal.h -rw-r--r-- root/root 1981 2021-02-03 10:22 ./usr/share/htslib-test/hts_os.c -rw-r--r-- root/root 5886 2022-07-19 11:03 ./usr/share/htslib-test/hts_time_funcs.h lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/htscodecs.mk -> htscodecs_external.mk -rw-r--r-- root/root 3675 2023-03-15 11:45 ./usr/share/htslib-test/htscodecs_bundled.mk -rw-r--r-- root/root 1710 2021-02-25 16:36 ./usr/share/htslib-test/htscodecs_external.mk -rw-r--r-- root/root 9547 2025-05-01 08:41 ./usr/share/htslib-test/htsfile.c -rw-r--r-- root/root 6976 2023-05-18 14:41 ./usr/share/htslib-test/htslib.mk -rw-r--r-- root/root 484 2024-10-17 18:24 ./usr/share/htslib-test/htslib.pc.in -rw-r--r-- root/root 180 2025-09-04 11:56 ./usr/share/htslib-test/htslib_static.mk -rw-r--r-- root/root 3333 2022-08-16 10:42 ./usr/share/htslib-test/htslib_vars.mk -rw-r--r-- root/root 10879 2021-02-03 10:22 ./usr/share/htslib-test/kfunc.c -rw-r--r-- root/root 11837 2024-04-05 09:17 ./usr/share/htslib-test/kstring.c drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/m4/ -rw-r--r-- root/root 2656 2023-11-08 17:07 ./usr/share/htslib-test/m4/hts_check_compile_flags_needed.m4 -rw-r--r-- root/root 4627 2025-04-17 09:02 ./usr/share/htslib-test/m4/hts_hide_dynamic_syms.m4 -rw-r--r-- root/root 8273 2019-04-18 12:14 ./usr/share/htslib-test/m4/hts_prog_cc_warnings.m4 -rw-r--r-- root/root 10244 2020-06-27 01:17 ./usr/share/htslib-test/m4/pkg.m4 -rw-r--r-- root/root 10656 2019-10-02 13:26 ./usr/share/htslib-test/md5.c -rw-r--r-- root/root 8488 2019-11-19 11:20 ./usr/share/htslib-test/multipart.c drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/os/ -rw-r--r-- root/root 2345 2017-04-26 20:08 ./usr/share/htslib-test/os/lzma_stub.h -rw-r--r-- root/root 2704 2019-10-01 22:06 ./usr/share/htslib-test/os/rand.c -rw-r--r-- root/root 6513 2023-03-29 16:35 ./usr/share/htslib-test/plugin.c -rw-r--r-- root/root 17284 2023-07-20 15:01 ./usr/share/htslib-test/probaln.c -rw-r--r-- root/root 13218 2023-05-23 14:36 ./usr/share/htslib-test/realn.c drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/ref_cache/ -rw-r--r-- root/root 2706 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/cmsg_wrap.c -rw-r--r-- root/root 1384 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/cmsg_wrap.h -rw-r--r-- root/root 21352 2025-05-23 16:45 ./usr/share/htslib-test/ref_cache/http_parser.c -rw-r--r-- root/root 3616 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/http_parser.h -rw-r--r-- root/root 7560 2025-05-23 16:37 ./usr/share/htslib-test/ref_cache/listener.c -rw-r--r-- root/root 1506 2025-05-09 15:35 ./usr/share/htslib-test/ref_cache/listener.h -rw-r--r-- root/root 9826 2025-05-27 22:43 ./usr/share/htslib-test/ref_cache/log_files.c -rw-r--r-- root/root 1723 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/log_files.h -rw-r--r-- root/root 35233 2025-06-11 09:28 ./usr/share/htslib-test/ref_cache/main.c -rw-r--r-- root/root 2331 2025-05-22 18:43 ./usr/share/htslib-test/ref_cache/misc.c -rw-r--r-- root/root 3263 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/misc.h -rw-r--r-- root/root 2940 2025-05-23 15:49 ./usr/share/htslib-test/ref_cache/options.h -rw-r--r-- root/root 4032 2025-05-23 16:37 ./usr/share/htslib-test/ref_cache/ping.c -rw-r--r-- root/root 1281 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/ping.h -rw-r--r-- root/root 2875 2025-05-26 20:37 ./usr/share/htslib-test/ref_cache/poll_wrap.h -rw-r--r-- root/root 3992 2025-05-26 21:33 ./usr/share/htslib-test/ref_cache/poll_wrap_epoll.c -rw-r--r-- root/root 7439 2025-05-26 21:30 ./usr/share/htslib-test/ref_cache/poll_wrap_poll.c -rw-r--r-- root/root 6061 2025-05-22 18:43 ./usr/share/htslib-test/ref_cache/ref_files.c -rw-r--r-- root/root 2361 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/ref_files.h -rw-r--r-- root/root 5655 2025-05-26 20:22 ./usr/share/htslib-test/ref_cache/request_handler.c -rw-r--r-- root/root 1595 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/request_handler.h -rw-r--r-- root/root 3112 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/sendfile_wrap.c -rw-r--r-- root/root 1634 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/sendfile_wrap.h -rw-r--r-- root/root 27805 2025-06-11 09:18 ./usr/share/htslib-test/ref_cache/server.c -rw-r--r-- root/root 1608 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/server.h -rw-r--r-- root/root 26960 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/transaction.c -rw-r--r-- root/root 3055 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/transaction.h -rw-r--r-- root/root 1588 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/types.h -rw-r--r-- root/root 37250 2025-05-31 19:55 ./usr/share/htslib-test/ref_cache/upstream.c -rw-r--r-- root/root 1734 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/upstream.h -rw-r--r-- root/root 20001 2023-05-30 10:31 ./usr/share/htslib-test/regidx.c -rw-r--r-- root/root 7744 2019-10-02 13:26 ./usr/share/htslib-test/region.c -rw-r--r-- root/root 205581 2025-09-04 11:56 ./usr/share/htslib-test/sam.c -rw-r--r-- root/root 4000 2025-02-09 20:20 ./usr/share/htslib-test/sam_internal.h -rw-r--r-- root/root 25791 2024-04-05 09:17 ./usr/share/htslib-test/sam_mods.c -rw-r--r-- root/root 9098 2024-09-23 15:22 ./usr/share/htslib-test/simd.c -rw-r--r-- root/root 50377 2024-12-20 21:02 ./usr/share/htslib-test/synced_bcf_reader.c -rw-r--r-- root/root 30342 2025-05-01 08:41 ./usr/share/htslib-test/tabix.c -rw-r--r-- root/root 22460 2025-03-31 17:52 ./usr/share/htslib-test/tbx.c drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/test/ drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/annot-tsv/ -rw-r--r-- root/root 38 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.1.txt -rw-r--r-- root/root 48 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.10.txt -rw-r--r-- root/root 59 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/dst.11.txt -rw-r--r-- root/root 59 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/dst.12.txt -rw-r--r-- root/root 12 2025-03-07 15:29 ./usr/share/htslib-test/test/annot-tsv/dst.14.txt -rw-r--r-- root/root 20 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.2.txt -rw-r--r-- root/root 38 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.3.txt -rw-r--r-- root/root 61 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.4.txt -rw-r--r-- root/root 62 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.5.txt -rw-r--r-- root/root 36 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.6.txt -rw-r--r-- root/root 27 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.7.txt -rw-r--r-- root/root 91 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.8.txt -rw-r--r-- root/root 49 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/dst.9.txt -rw-r--r-- root/root 69 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.1.1.txt -rw-r--r-- root/root 67 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.1.2.txt -rw-r--r-- root/root 88 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.1.3.txt -rw-r--r-- root/root 67 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.1.4.txt -rw-r--r-- root/root 65 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.1.5.txt -rw-r--r-- root/root 67 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.1.6.txt -rw-r--r-- root/root 60 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.10.1.txt -rw-r--r-- root/root 50 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.10.2.txt -rw-r--r-- root/root 40 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.10.3.txt -rw-r--r-- root/root 60 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.10.4.txt -rw-r--r-- root/root 40 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.10.5.txt -rw-r--r-- root/root 50 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.10.6.txt -rw-r--r-- root/root 36 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/out.11.1.txt -rw-r--r-- root/root 78 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/out.11.2.txt -rw-r--r-- root/root 63 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/out.11.3.txt -rw-r--r-- root/root 36 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/out.12.1.txt -rw-r--r-- root/root 49 2024-07-23 13:26 ./usr/share/htslib-test/test/annot-tsv/out.13.1.txt -rw-r--r-- root/root 38 2024-07-23 13:26 ./usr/share/htslib-test/test/annot-tsv/out.13.2.txt -rw-r--r-- root/root 43 2024-07-23 13:26 ./usr/share/htslib-test/test/annot-tsv/out.13.3.txt -rw-r--r-- root/root 44 2024-07-23 13:26 ./usr/share/htslib-test/test/annot-tsv/out.13.4.txt -rw-r--r-- root/root 12 2025-03-07 15:29 ./usr/share/htslib-test/test/annot-tsv/out.14.1.txt -rw-r--r-- root/root 6 2025-03-07 15:29 ./usr/share/htslib-test/test/annot-tsv/out.14.2.txt -rw-r--r-- root/root 28 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.2.1.txt -rw-r--r-- root/root 26 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.2.2.txt -rw-r--r-- root/root 38 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.2.3.txt -rw-r--r-- root/root 38 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.2.4.txt -rw-r--r-- root/root 46 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.2.5.txt -rw-r--r-- root/root 26 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.2.6.txt -rw-r--r-- root/root 97 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.3.1.txt -rw-r--r-- root/root 87 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.4.1.txt -rw-r--r-- root/root 95 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.5.1.txt -rw-r--r-- root/root 48 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.6.1.txt -rw-r--r-- root/root 42 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.7.1.txt -rw-r--r-- root/root 135 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.8.1.txt -rw-r--r-- root/root 111 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/out.9.1.txt -rw-r--r-- root/root 58 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.1.txt -rw-r--r-- root/root 38 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.10.txt -rw-r--r-- root/root 75 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/src.11.txt -rw-r--r-- root/root 75 2024-04-30 14:29 ./usr/share/htslib-test/test/annot-tsv/src.12.txt -rw-r--r-- root/root 27 2024-07-23 13:26 ./usr/share/htslib-test/test/annot-tsv/src.13.txt -rw-r--r-- root/root 12 2025-03-07 15:29 ./usr/share/htslib-test/test/annot-tsv/src.14.txt -rw-r--r-- root/root 40 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.2.txt -rw-r--r-- root/root 58 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.3.txt -rw-r--r-- root/root 73 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.4.txt -rw-r--r-- root/root 62 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.5.txt -rw-r--r-- root/root 18 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.6.txt -rw-r--r-- root/root 18 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.7.txt -rw-r--r-- root/root 94 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.8.txt -rw-r--r-- root/root 36 2023-05-18 14:41 ./usr/share/htslib-test/test/annot-tsv/src.9.txt -rw-r--r-- root/root 751 2016-06-17 10:40 ./usr/share/htslib-test/test/auxf#values.sam -rw-r--r-- root/root 5152 2016-10-20 13:38 ./usr/share/htslib-test/test/auxf#values_java.cram -rw-r--r-- root/root 29 2014-12-20 14:53 ./usr/share/htslib-test/test/auxf.fa -rw-r--r-- root/root 18 2014-12-20 14:53 ./usr/share/htslib-test/test/auxf.fa.fai drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/base_mods/ -rw-r--r-- root/root 739 2023-05-02 11:04 ./usr/share/htslib-test/test/base_mods/MM-MNf1.sam -rw-r--r-- root/root 739 2023-05-02 11:04 ./usr/share/htslib-test/test/base_mods/MM-MNf2.sam -rw-r--r-- root/root 739 2023-05-02 11:04 ./usr/share/htslib-test/test/base_mods/MM-MNp.sam -rw-r--r-- root/root 193 2024-02-13 13:55 ./usr/share/htslib-test/test/base_mods/MM-bounds+.sam -rw-r--r-- root/root 195 2024-02-13 13:55 ./usr/share/htslib-test/test/base_mods/MM-bounds-.sam -rw-r--r-- root/root 372 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-chebi.out -rw-r--r-- root/root 172 2024-02-13 13:55 ./usr/share/htslib-test/test/base_mods/MM-chebi.sam -rw-r--r-- root/root 343 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-double.out -rw-r--r-- root/root 254 2020-08-19 08:34 ./usr/share/htslib-test/test/base_mods/MM-double.sam -rw-r--r-- root/root 924 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-explicit-f.out -rw-r--r-- root/root 791 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-explicit-x.out -rw-r--r-- root/root 768 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-explicit.out -rw-r--r-- root/root 1083 2024-07-18 01:25 ./usr/share/htslib-test/test/base_mods/MM-explicit.sam -rw-r--r-- root/root 765 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-multi.out -rw-r--r-- root/root 537 2023-05-02 11:04 ./usr/share/htslib-test/test/base_mods/MM-multi.sam -rw-r--r-- root/root 1096 2023-07-14 08:15 ./usr/share/htslib-test/test/base_mods/MM-not-all-modded.out -rw-r--r-- root/root 558 2023-07-13 13:42 ./usr/share/htslib-test/test/base_mods/MM-not-all-modded.sam -rw-r--r-- root/root 510 2020-08-19 08:34 ./usr/share/htslib-test/test/base_mods/MM-orient.sam -rw-r--r-- root/root 713 2020-08-19 08:34 ./usr/share/htslib-test/test/base_mods/MM-pileup.out -rw-r--r-- root/root 723 2020-08-19 08:34 ./usr/share/htslib-test/test/base_mods/MM-pileup.sam -rw-r--r-- root/root 518 2020-08-19 08:34 ./usr/share/htslib-test/test/base_mods/MM-pileup2.out -rw-r--r-- root/root 372 2020-08-19 08:34 ./usr/share/htslib-test/test/base_mods/MM-pileup2.sam -rwxr-xr-x root/root 1331 2020-08-28 11:29 ./usr/share/htslib-test/test/base_mods/base-mods.sh -rw-r--r-- root/root 2717 2024-02-13 13:55 ./usr/share/htslib-test/test/base_mods/base-mods.tst drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/bcf-sr/ -rw-r--r-- root/root 518 2020-07-01 17:33 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.a.vcf -rw-r--r-- root/root 128 2020-07-01 17:33 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.abc.expected.out -rw-r--r-- root/root 634 2020-07-01 17:33 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.b.vcf -rw-r--r-- root/root 634 2020-07-01 17:33 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.c.vcf -rw-r--r-- root/root 518 2020-07-01 17:33 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.hdr_order.vcf -rw-r--r-- root/root 518 2020-07-01 17:33 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.rec_order.vcf -rw-r--r-- root/root 217 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.1.out -rw-r--r-- root/root 201 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.2.out -rw-r--r-- root/root 221 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.3.out -rw-r--r-- root/root 203 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.4.out -rw-r--r-- root/root 225 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.5.out -rw-r--r-- root/root 205 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.6.out -rw-r--r-- root/root 241 2023-06-20 11:25 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.vcf drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/bgzf_boundaries/ -rw-r--r-- root/root 432 2024-06-04 10:38 ./usr/share/htslib-test/test/bgzf_boundaries/bgzf_boundaries1.bam -rw-r--r-- root/root 432 2024-06-04 10:38 ./usr/share/htslib-test/test/bgzf_boundaries/bgzf_boundaries2.bam -rw-r--r-- root/root 897 2024-06-04 10:38 ./usr/share/htslib-test/test/bgzf_boundaries/bgzf_boundaries3.bam -rw-r--r-- root/root 15 2016-09-01 13:22 ./usr/share/htslib-test/test/bgziptest.txt -rw-r--r-- root/root 181 2025-09-04 11:56 ./usr/share/htslib-test/test/bgziptest.txt.gz -rw-r--r-- root/root 88 2016-09-01 13:22 ./usr/share/htslib-test/test/bgziptest.txt.gz.gzi -rw-r--r-- root/root 148 2013-09-20 08:58 ./usr/share/htslib-test/test/c1#bounds.sam -rw-r--r-- root/root 337 2013-07-22 11:08 ./usr/share/htslib-test/test/c1#clip.sam -rw-r--r-- root/root 433 2015-04-08 15:41 ./usr/share/htslib-test/test/c1#noseq.sam -rw-r--r-- root/root 388 2013-07-22 11:08 ./usr/share/htslib-test/test/c1#pad1.sam -rw-r--r-- root/root 527 2015-02-18 10:27 ./usr/share/htslib-test/test/c1#pad2.sam -rw-r--r-- root/root 665 2015-02-18 10:27 ./usr/share/htslib-test/test/c1#pad3.sam -rw-r--r-- root/root 429 2015-03-10 15:05 ./usr/share/htslib-test/test/c1#unknown.sam -rw-r--r-- root/root 15 2013-07-22 11:08 ./usr/share/htslib-test/test/c1.fa -rw-r--r-- root/root 14 2013-07-22 11:08 ./usr/share/htslib-test/test/c1.fa.fai -rw-r--r-- root/root 847 2015-04-29 13:55 ./usr/share/htslib-test/test/c2#pad.sam -rw-r--r-- root/root 14 2015-04-29 14:19 ./usr/share/htslib-test/test/c2.fa -rw-r--r-- root/root 12 2015-04-29 14:24 ./usr/share/htslib-test/test/c2.fa.fai -rw-r--r-- root/root 341 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#1.sam -rw-r--r-- root/root 322632 2018-03-09 11:50 ./usr/share/htslib-test/test/ce#1000.sam -rw-r--r-- root/root 645 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#2.sam -rw-r--r-- root/root 1872 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#5.sam -rw-r--r-- root/root 1836 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#5b.sam -rw-r--r-- root/root 6784 2016-03-18 14:17 ./usr/share/htslib-test/test/ce#5b_java.cram -rw-r--r-- root/root 2147244 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#large_seq.sam -rw-r--r-- root/root 547 2015-04-08 16:32 ./usr/share/htslib-test/test/ce#supp.sam -rw-r--r-- root/root 1638 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#tag_depadded.sam -rw-r--r-- root/root 1650 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#tag_padded.sam -rw-r--r-- root/root 1325 2013-07-22 11:08 ./usr/share/htslib-test/test/ce#unmap.sam -rw-r--r-- root/root 2747 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#unmap1.sam -rw-r--r-- root/root 5525 2015-02-18 10:27 ./usr/share/htslib-test/test/ce#unmap2.sam -rw-r--r-- root/root 1060702 2013-07-22 11:08 ./usr/share/htslib-test/test/ce.fa -rw-r--r-- root/root 230 2013-07-22 11:08 ./usr/share/htslib-test/test/ce.fa.fai -rw-r--r-- root/root 268 2018-06-07 10:50 ./usr/share/htslib-test/test/colons.bam -rw-r--r-- root/root 424 2018-06-07 10:50 ./usr/share/htslib-test/test/colons.bam.bai -rwxr-xr-x root/root 6549 2025-09-04 11:56 ./usr/share/htslib-test/test/compare_sam.pl -rwxr-xr-x root/root 4307 2019-11-19 11:20 ./usr/share/htslib-test/test/cross_validate.sh -rw-r--r-- root/root 0 2019-08-28 14:58 ./usr/share/htslib-test/test/emptyfile drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/faidx/ -rw-r--r-- root/root 326 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/ce.1.expected.fa -rw-r--r-- root/root 94 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/faidx.1.expected.fa -rw-r--r-- root/root 289 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/faidx.fa -rw-r--r-- root/root 117 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/faidx.fa.expected.fai -rw-r--r-- root/root 4437 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/faidx.tst -rw-r--r-- root/root 336 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/fastqs.1.expected.fq -rw-r--r-- root/root 225 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/fastqs.2.expected.fa -rw-r--r-- root/root 48599 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/fastqs.fq -rw-r--r-- root/root 3750 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/fastqs.fq.expected.fai -rwxr-xr-x root/root 1314 2022-11-02 15:57 ./usr/share/htslib-test/test/faidx/test-faidx.sh drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/fastq/ -rw-r--r-- root/root 4549 2022-08-10 14:14 ./usr/share/htslib-test/test/fastq/fastq.tst -rw-r--r-- root/root 667 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/filter_casava-q.sam -rw-r--r-- root/root 596 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/filter_casava.fa -rw-r--r-- root/root 1008 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/filter_casava.fq -rw-r--r-- root/root 1063 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/filter_casava.sam -rw-r--r-- root/root 1765 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/inter_aux-q.sam -rw-r--r-- root/root 2755 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/inter_aux.sam -rw-r--r-- root/root 1665 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/inter_casava-q.sam -rw-r--r-- root/root 2655 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/inter_casava.sam -rw-r--r-- root/root 1665 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/inter_casavaOX-q.sam -rw-r--r-- root/root 2655 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/inter_casavaOX.sam -rw-r--r-- root/root 1525 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/inter_noaux-q.sam -rw-r--r-- root/root 2515 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/inter_noaux.sam -rw-r--r-- root/root 1600 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/interleaved.fa -rw-r--r-- root/root 2630 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/interleaved.fq -rw-r--r-- root/root 1490 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/interleaved_casava.fa -rw-r--r-- root/root 2520 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/interleaved_casava.fq -rw-r--r-- root/root 1052 2022-08-10 14:14 ./usr/share/htslib-test/test/fastq/longline.fq -rw-r--r-- root/root 1065 2022-08-10 14:14 ./usr/share/htslib-test/test/fastq/longline.sam -rw-r--r-- root/root 22 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/minimal-q.sam -rw-r--r-- root/root 5 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/minimal.fa -rw-r--r-- root/root 9 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/minimal.fq -rw-r--r-- root/root 22 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/minimal.sam -rw-r--r-- root/root 126 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/multiline-q.sam -rw-r--r-- root/root 98 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/multiline.fa -rw-r--r-- root/root 188 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/multiline.fq -rw-r--r-- root/root 202 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/multiline.sam -rw-r--r-- root/root 512 2021-09-22 11:38 ./usr/share/htslib-test/test/fastq/name2-q.sam -rw-r--r-- root/root 482 2021-09-22 11:38 ./usr/share/htslib-test/test/fastq/name2.fa -rw-r--r-- root/root 894 2021-09-22 11:38 ./usr/share/htslib-test/test/fastq/name2.fq -rw-r--r-- root/root 908 2021-09-22 11:38 ./usr/share/htslib-test/test/fastq/name2.sam -rw-r--r-- root/root 950 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/r1-q.sam -rw-r--r-- root/root 870 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/r1.fa -rw-r--r-- root/root 1385 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/r1.fq -rw-r--r-- root/root 1445 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/r1.sam -rw-r--r-- root/root 815 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/r2-q.sam -rw-r--r-- root/root 730 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/r2.fa -rw-r--r-- root/root 1245 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/r2.fq -rw-r--r-- root/root 1310 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/r2.sam -rw-r--r-- root/root 720 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/single.fa -rw-r--r-- root/root 1235 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/single.fq -rw-r--r-- root/root 805 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/single_aux-q.sam -rw-r--r-- root/root 1300 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/single_aux.sam -rw-r--r-- root/root 755 2020-10-19 14:07 ./usr/share/htslib-test/test/fastq/single_noaux-q.sam -rw-r--r-- root/root 1250 2020-10-01 15:16 ./usr/share/htslib-test/test/fastq/single_noaux.sam -rwxr-xr-x root/root 1318 2020-10-13 14:23 ./usr/share/htslib-test/test/fastq/test-fastq.sh -rw-r--r-- root/root 4951 2018-05-21 14:09 ./usr/share/htslib-test/test/fastqs_README.txt -rw-r--r-- root/root 2438 2020-01-07 15:32 ./usr/share/htslib-test/test/fieldarith.c -rw-r--r-- root/root 910 2020-05-18 14:27 ./usr/share/htslib-test/test/fieldarith.sam -rw-r--r-- root/root 241 2021-02-16 16:49 ./usr/share/htslib-test/test/formatcols.vcf -rw-r--r-- root/root 226 2016-09-09 09:11 ./usr/share/htslib-test/test/formatmissing-out.vcf -rw-r--r-- root/root 226 2016-09-09 09:11 ./usr/share/htslib-test/test/formatmissing.vcf drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/test/fuzz/ -rw-r--r-- root/root 5618 2025-09-04 11:56 ./usr/share/htslib-test/test/fuzz/hts_open_fuzzer.c -rwxr-xr-x root/root 3581 2025-09-04 11:56 ./usr/share/htslib-test/test/header_syms.pl -rw-r--r-- root/root 12062 2024-08-15 15:14 ./usr/share/htslib-test/test/hfile.c -rw-r--r-- root/root 17620 2020-01-07 15:32 ./usr/share/htslib-test/test/hts_endian.c -rw-r--r-- root/root 776 2019-01-30 14:48 ./usr/share/htslib-test/test/index.bam.bai -rw-r--r-- root/root 130 2019-01-30 14:48 ./usr/share/htslib-test/test/index.bam.csi -rw-r--r-- root/root 144 2024-02-07 12:36 ./usr/share/htslib-test/test/index.bcf.csi -rw-r--r-- root/root 83 2019-01-30 14:48 ./usr/share/htslib-test/test/index.cram.crai -rw-r--r-- root/root 54185 2019-01-30 14:48 ./usr/share/htslib-test/test/index.sam -rw-r--r-- root/root 776 2019-01-30 14:48 ./usr/share/htslib-test/test/index.sam.gz.bai -rw-r--r-- root/root 130 2019-01-30 14:48 ./usr/share/htslib-test/test/index.sam.gz.csi -rw-r--r-- root/root 68888 2018-06-20 13:11 ./usr/share/htslib-test/test/index.vcf -rw-r--r-- root/root 168 2022-01-20 16:28 ./usr/share/htslib-test/test/index.vcf.gz.csi -rw-r--r-- root/root 206 2022-01-20 16:28 ./usr/share/htslib-test/test/index.vcf.gz.tbi -rw-r--r-- root/root 477 2021-11-03 14:46 ./usr/share/htslib-test/test/index2.sam -rw-r--r-- root/root 54375 2020-10-07 12:00 ./usr/share/htslib-test/test/index_dos.sam drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/longrefs/ -rw-r--r-- root/root 594 2019-09-11 09:29 ./usr/share/htslib-test/test/longrefs/index.expected1.vcf -rw-r--r-- root/root 83 2019-12-09 14:05 ./usr/share/htslib-test/test/longrefs/index.expected2.vcf -rw-r--r-- root/root 21491 2019-12-09 14:05 ./usr/share/htslib-test/test/longrefs/index.vcf -rw-r--r-- root/root 31717 2019-09-10 11:27 ./usr/share/htslib-test/test/longrefs/longref.sam -rw-r--r-- root/root 8300 2019-09-10 11:27 ./usr/share/htslib-test/test/longrefs/longref_itr.expected.sam -rw-r--r-- root/root 15015 2019-09-10 11:27 ./usr/share/htslib-test/test/longrefs/longref_multi.expected.sam drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/test/maintainer/ -rwxr-xr-x root/root 3292 2025-09-04 11:56 ./usr/share/htslib-test/test/maintainer/check_copyright.pl -rwxr-xr-x root/root 2734 2025-09-04 11:56 ./usr/share/htslib-test/test/maintainer/check_spaces.pl -rw-r--r-- root/root 1017 2016-05-20 13:59 ./usr/share/htslib-test/test/md#1.sam -rw-r--r-- root/root 45 2016-05-20 13:59 ./usr/share/htslib-test/test/md.fa -rw-r--r-- root/root 13 2016-05-20 13:59 ./usr/share/htslib-test/test/md.fa.fai -rw-r--r-- root/root 148 2023-01-06 16:58 ./usr/share/htslib-test/test/modhdr.expected.vcf -rw-r--r-- root/root 156 2025-09-04 11:56 ./usr/share/htslib-test/test/modhdr.vcf.gz -rw-r--r-- root/root 86 2023-01-06 16:58 ./usr/share/htslib-test/test/modhdr.vcf.gz.csi drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/mpileup/ -rw-r--r-- root/root 374 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/c1#pad1.out -rw-r--r-- root/root 2024 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/c1#pad1.sam -rw-r--r-- root/root 486 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/c1#pad2.out -rw-r--r-- root/root 2311 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/c1#pad2.sam -rw-r--r-- root/root 194 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/c1#pad3.out -rw-r--r-- root/root 2393 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/c1#pad3.sam -rw-r--r-- root/root 174 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_D.out -rw-r--r-- root/root 1534 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/mp_D.sam -rw-r--r-- root/root 261 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_DI.out -rw-r--r-- root/root 1747 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/mp_DI.sam -rw-r--r-- root/root 179 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_I.out -rw-r--r-- root/root 1821 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/mp_I.sam -rw-r--r-- root/root 241 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_ID.out -rw-r--r-- root/root 1958 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/mp_ID.sam -rw-r--r-- root/root 166 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_N.out -rw-r--r-- root/root 1739 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/mp_N.sam -rw-r--r-- root/root 366 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_N2.out -rw-r--r-- root/root 2152 2020-10-27 13:45 ./usr/share/htslib-test/test/mpileup/mp_N2.sam -rw-r--r-- root/root 229 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_P.out -rw-r--r-- root/root 1796 2018-09-21 09:25 ./usr/share/htslib-test/test/mpileup/mp_P.sam -rw-r--r-- root/root 214 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_overlap1.out -rw-r--r-- root/root 149 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_overlap1.sam -rw-r--r-- root/root 214 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_overlap2.out -rw-r--r-- root/root 149 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mp_overlap2.sam -rw-r--r-- root/root 2725 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/mpileup.tst -rw-r--r-- root/root 1294 2019-06-18 09:13 ./usr/share/htslib-test/test/mpileup/small.bam -rw-r--r-- root/root 4171 2024-02-16 14:04 ./usr/share/htslib-test/test/mpileup/small.out -rwxr-xr-x root/root 1295 2019-11-19 11:20 ./usr/share/htslib-test/test/mpileup/test-pileup.sh -rw-r--r-- root/root 1691 2019-07-04 15:43 ./usr/share/htslib-test/test/no_hdr_sq_1.bam -rw-r--r-- root/root 94 2019-07-04 15:43 ./usr/share/htslib-test/test/no_hdr_sq_1.bam.csi -rw-r--r-- root/root 2019 2019-07-04 15:43 ./usr/share/htslib-test/test/no_hdr_sq_1.expected.sam -rw-r--r-- root/root 404 2024-03-20 10:11 ./usr/share/htslib-test/test/noroundtrip-out.vcf -rw-r--r-- root/root 367 2024-03-20 10:11 ./usr/share/htslib-test/test/noroundtrip.vcf -rw-r--r-- root/root 7459 2024-04-05 09:17 ./usr/share/htslib-test/test/pileup.c -rw-r--r-- root/root 7161 2024-02-19 17:12 ./usr/share/htslib-test/test/pileup_mod.c -rw-r--r-- root/root 5076 2024-04-29 14:17 ./usr/share/htslib-test/test/plugins-dlhts.c -rw-r--r-- root/root 13337 2018-01-31 12:22 ./usr/share/htslib-test/test/range.bam -rw-r--r-- root/root 360 2018-01-31 12:22 ./usr/share/htslib-test/test/range.bam.bai -rw-r--r-- root/root 11182 2018-01-31 12:22 ./usr/share/htslib-test/test/range.cram -rw-r--r-- root/root 94 2018-01-31 12:22 ./usr/share/htslib-test/test/range.cram.crai -rw-r--r-- root/root 3496 2018-01-31 12:22 ./usr/share/htslib-test/test/range.out -rw-r--r-- root/root 4833 2024-06-03 12:54 ./usr/share/htslib-test/test/range.out2 -rw-r--r-- root/root 719 2018-02-09 10:23 ./usr/share/htslib-test/test/realn01.fa -rw-r--r-- root/root 21 2018-02-09 10:23 ./usr/share/htslib-test/test/realn01.fa.fai -rw-r--r-- root/root 1843 2018-02-09 10:23 ./usr/share/htslib-test/test/realn01.sam -rw-r--r-- root/root 2157 2018-02-09 10:23 ./usr/share/htslib-test/test/realn01_exp-a.sam -rw-r--r-- root/root 2157 2018-02-09 10:23 ./usr/share/htslib-test/test/realn01_exp-e.sam -rw-r--r-- root/root 2157 2018-02-09 10:23 ./usr/share/htslib-test/test/realn01_exp.sam -rw-r--r-- root/root 3758 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02-r.sam -rw-r--r-- root/root 4284 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02.fa -rw-r--r-- root/root 17 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02.fa.fai -rw-r--r-- root/root 2894 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02.sam -rw-r--r-- root/root 3758 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02_exp-a.sam -rw-r--r-- root/root 3758 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02_exp-e.sam -rw-r--r-- root/root 3758 2018-02-09 10:23 ./usr/share/htslib-test/test/realn02_exp.sam -rw-r--r-- root/root 16 2023-05-23 14:36 ./usr/share/htslib-test/test/realn03.fa -rw-r--r-- root/root 14 2023-05-23 14:36 ./usr/share/htslib-test/test/realn03.fa.fai -rw-r--r-- root/root 138 2023-05-23 14:36 ./usr/share/htslib-test/test/realn03.sam -rw-r--r-- root/root 172 2023-05-23 14:36 ./usr/share/htslib-test/test/realn03_exp.sam drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/ref_cache/ -rw-r--r-- root/root 2016 2025-04-17 09:02 ./usr/share/htslib-test/test/ref_cache/ce_m5.sam -rw-r--r-- root/root 84621 2024-10-07 13:30 ./usr/share/htslib-test/test/sam.c drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/sam_filter/ -rwxr-xr-x root/root 1291 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/filter.sh -rw-r--r-- root/root 2927 2023-08-09 11:01 ./usr/share/htslib-test/test/sam_filter/filter.tst -rw-r--r-- root/root 2 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/func1.out -rw-r--r-- root/root 3 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/func2.out -rw-r--r-- root/root 2 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/func3.out -rw-r--r-- root/root 4 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/func4.out -rw-r--r-- root/root 1552 2022-05-27 11:19 ./usr/share/htslib-test/test/sam_filter/func5.out -rw-r--r-- root/root 585 2022-05-27 11:19 ./usr/share/htslib-test/test/sam_filter/func6.out -rw-r--r-- root/root 946 2022-05-27 11:19 ./usr/share/htslib-test/test/sam_filter/func7.out -rw-r--r-- root/root 40 2023-08-09 11:01 ./usr/share/htslib-test/test/sam_filter/func8.out -rw-r--r-- root/root 3 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/int1.out -rw-r--r-- root/root 3 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/int2.out -rw-r--r-- root/root 3 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/int3.out -rw-r--r-- root/root 485 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/string1.out -rw-r--r-- root/root 451 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/string2.out -rw-r--r-- root/root 748 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/string3.out -rw-r--r-- root/root 1136 2020-11-23 12:22 ./usr/share/htslib-test/test/sam_filter/string4.out -rw-r--r-- root/root 498 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/string5.out -rw-r--r-- root/root 319 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/string6.out -rw-r--r-- root/root 410 2020-11-30 16:43 ./usr/share/htslib-test/test/sam_filter/string7.out -rwxr-xr-x root/root 5728 2023-07-14 08:06 ./usr/share/htslib-test/test/simple_test_driver.sh -rw-r--r-- root/root 98 2019-04-18 15:36 ./usr/share/htslib-test/test/tabix.out drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/test/tabix/ -rw-r--r-- root/root 47 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/bed_file.Y.100200.out -rw-r--r-- root/root 1857 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/bed_file.bed -rw-r--r-- root/root 407 2020-07-28 14:59 ./usr/share/htslib-test/test/tabix/bed_file.separate.out -rw-r--r-- root/root 405 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/gff_file.X.2934832.2935190.out -rw-r--r-- root/root 5618 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/gff_file.gff -rw-r--r-- root/root 288 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/large_chr.20.1.2147483647.out -rw-r--r-- root/root 622 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/large_chr.vcf -rw-r--r-- root/root 3193 2024-02-29 10:18 ./usr/share/htslib-test/test/tabix/tabix.tst -rwxr-xr-x root/root 1312 2019-11-19 11:20 ./usr/share/htslib-test/test/tabix/test-tabix.sh -rw-r--r-- root/root 67 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/vcf_file.1.3000151.out -rw-r--r-- root/root 74 2017-02-13 11:57 ./usr/share/htslib-test/test/tabix/vcf_file.2.3199812.out -rw-r--r-- root/root 4485 2022-08-13 21:16 ./usr/share/htslib-test/test/tabix/vcf_file.bcf -rw-r--r-- root/root 4302 2022-08-13 21:16 ./usr/share/htslib-test/test/tabix/vcf_file.vcf -rw-r--r-- root/root 10950 2024-12-20 21:02 ./usr/share/htslib-test/test/test-bcf-sr.c -rwxr-xr-x root/root 17395 2025-09-04 11:56 ./usr/share/htslib-test/test/test-bcf-sr.pl -rw-r--r-- root/root 8997 2024-08-15 15:14 ./usr/share/htslib-test/test/test-bcf-translate.c -rw-r--r-- root/root 869 2017-08-29 09:56 ./usr/share/htslib-test/test/test-bcf-translate.out -rw-r--r-- root/root 4362 2025-05-01 08:41 ./usr/share/htslib-test/test/test-bcf_set_variant_type.c -rwxr-xr-x root/root 2601 2025-09-04 11:56 ./usr/share/htslib-test/test/test-logging.pl -rw-r--r-- root/root 7064 2020-01-07 15:32 ./usr/share/htslib-test/test/test-parse-reg.c -rw-r--r-- root/root 16999 2023-07-20 15:01 ./usr/share/htslib-test/test/test-regidx.c -rw-r--r-- root/root 32136 2025-03-31 17:52 ./usr/share/htslib-test/test/test-vcf-api.c -rw-r--r-- root/root 2064 2019-04-10 11:40 ./usr/share/htslib-test/test/test-vcf-api.out -rw-r--r-- root/root 2024 2016-03-24 11:32 ./usr/share/htslib-test/test/test-vcf-hdr-in.vcf -rw-r--r-- root/root 1349 2016-03-24 11:32 ./usr/share/htslib-test/test/test-vcf-hdr.out -rw-r--r-- root/root 3840 2021-01-29 18:34 ./usr/share/htslib-test/test/test-vcf-sweep.c -rw-r--r-- root/root 92 2013-09-05 09:41 ./usr/share/htslib-test/test/test-vcf-sweep.out -rwxr-xr-x root/root 67806 2025-09-04 11:56 ./usr/share/htslib-test/test/test.pl -rw-r--r-- root/root 36977 2024-08-15 14:18 ./usr/share/htslib-test/test/test_bgzf.c -rw-r--r-- root/root 12549 2022-07-14 09:33 ./usr/share/htslib-test/test/test_expr.c -rw-r--r-- root/root 16603 2024-07-18 01:25 ./usr/share/htslib-test/test/test_faidx.c -rw-r--r-- root/root 2869 2020-10-23 14:06 ./usr/share/htslib-test/test/test_index.c -rw-r--r-- root/root 3313 2021-06-22 10:24 ./usr/share/htslib-test/test/test_introspection.c -rw-r--r-- root/root 3639 2020-08-17 16:18 ./usr/share/htslib-test/test/test_kfunc.c -rw-r--r-- root/root 13558 2025-04-04 07:38 ./usr/share/htslib-test/test/test_khash.c -rw-r--r-- root/root 18461 2025-03-24 10:00 ./usr/share/htslib-test/test/test_kstring.c -rw-r--r-- root/root 7628 2024-02-19 17:12 ./usr/share/htslib-test/test/test_mod.c -rw-r--r-- root/root 4542 2024-06-23 19:32 ./usr/share/htslib-test/test/test_nibbles.c -rw-r--r-- root/root 5057 2020-09-25 16:16 ./usr/share/htslib-test/test/test_realn.c -rw-r--r-- root/root 8892 2020-09-25 16:16 ./usr/share/htslib-test/test/test_str2int.c -rw-r--r-- root/root 4581 2022-08-16 17:05 ./usr/share/htslib-test/test/test_time_funcs.c -rw-r--r-- root/root 15046 2023-08-25 22:09 ./usr/share/htslib-test/test/test_view.c -rw-r--r-- root/root 1688 2020-01-07 15:32 ./usr/share/htslib-test/test/thrash_threads1.c -rw-r--r-- root/root 1621 2020-01-07 15:32 ./usr/share/htslib-test/test/thrash_threads2.c -rw-r--r-- root/root 1729 2020-01-07 15:32 ./usr/share/htslib-test/test/thrash_threads3.c -rw-r--r-- root/root 2310 2025-04-10 09:08 ./usr/share/htslib-test/test/thrash_threads4.c -rw-r--r-- root/root 2176 2020-01-07 15:32 ./usr/share/htslib-test/test/thrash_threads5.c -rw-r--r-- root/root 3452 2025-04-10 09:08 ./usr/share/htslib-test/test/thrash_threads6.c -rw-r--r-- root/root 3693 2025-04-10 09:08 ./usr/share/htslib-test/test/thrash_threads7.c -rw-r--r-- root/root 2938 2017-03-03 19:48 ./usr/share/htslib-test/test/thread_pool.md -rw-r--r-- root/root 2487 2023-10-03 19:09 ./usr/share/htslib-test/test/usepublic.cpp -rw-r--r-- root/root 1549 2025-03-24 10:00 ./usr/share/htslib-test/test/vcf44_1.expected -rw-r--r-- root/root 1511 2025-03-24 10:00 ./usr/share/htslib-test/test/vcf44_1.vcf -rw-r--r-- root/root 427 2021-04-09 16:58 ./usr/share/htslib-test/test/vcf_meta_meta.vcf -rwxr-xr-x root/root 2358 2025-04-17 09:02 ./usr/share/htslib-test/test/with-shlib.sh -rw-r--r-- root/root 1070 2018-11-07 11:03 ./usr/share/htslib-test/test/xx#MD.sam -rw-r--r-- root/root 1159 2018-11-07 11:03 ./usr/share/htslib-test/test/xx#MD2.sam -rw-r--r-- root/root 71 2019-08-28 14:58 ./usr/share/htslib-test/test/xx#blank.sam -rw-r--r-- root/root 905485 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#large_aux.sam -rw-r--r-- root/root 651 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#large_aux2.sam -rw-r--r-- root/root 22668 2016-03-18 14:17 ./usr/share/htslib-test/test/xx#large_aux_java.cram -rw-r--r-- root/root 254 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#minimal.sam -rw-r--r-- root/root 304 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#pair.sam -rw-r--r-- root/root 298 2016-01-14 12:15 ./usr/share/htslib-test/test/xx#repeated.sam -rw-r--r-- root/root 517 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#rg.sam -rw-r--r-- root/root 1028 2015-04-29 13:55 ./usr/share/htslib-test/test/xx#tlen.sam -rw-r--r-- root/root 1096 2015-04-29 13:55 ./usr/share/htslib-test/test/xx#tlen2.sam -rw-r--r-- root/root 267 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#triplet.sam -rw-r--r-- root/root 134 2024-10-24 08:55 ./usr/share/htslib-test/test/xx#u.sam -rw-r--r-- root/root 320 2013-07-22 11:08 ./usr/share/htslib-test/test/xx#unsorted.sam -rw-r--r-- root/root 86 2018-11-07 11:03 ./usr/share/htslib-test/test/xx.fa -rw-r--r-- root/root 44 2018-11-07 11:03 ./usr/share/htslib-test/test/xx.fa.fai -rw-r--r-- root/root 11998 2024-04-29 14:17 ./usr/share/htslib-test/textutils.c -rw-r--r-- root/root 15642 2024-04-05 09:17 ./usr/share/htslib-test/textutils_internal.h -rw-r--r-- root/root 46000 2025-04-10 09:08 ./usr/share/htslib-test/thread_pool.c -rw-r--r-- root/root 5853 2019-03-04 12:44 ./usr/share/htslib-test/thread_pool_internal.h -rw-r--r-- root/root 219598 2025-05-19 11:00 ./usr/share/htslib-test/vcf.c -rw-r--r-- root/root 5570 2020-07-11 11:34 ./usr/share/htslib-test/vcf_sweep.c -rw-r--r-- root/root 34891 2022-02-10 10:46 ./usr/share/htslib-test/vcfutils.c -rwxr-xr-x root/root 2233 2025-09-04 11:56 ./usr/share/htslib-test/version.sh drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 313 2024-11-14 19:27 ./usr/share/lintian/overrides/htslib-test libhts-dev_1.22.1+ds2-1_amd64.deb --------------------------------- new Debian package, version 2.0. size 1784944 bytes: control archive=2024 bytes. 1234 bytes, 27 lines control 2420 bytes, 37 lines md5sums Package: libhts-dev Source: htslib Version: 1.22.1+ds2-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 7564 Depends: libbz2-dev, libhts3t64 (= 1.22.1+ds2-1), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, zlib1g-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. . For compatibility with sambamba, the internal routine cram_to_bam was exported, hereto adopting a patch found in guix. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/include/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/include/htslib/ -rw-r--r-- root/root 17826 2025-02-15 22:49 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 24614 2024-08-15 14:18 ./usr/include/htslib/cram.h -rw-r--r-- root/root 15122 2023-07-20 15:01 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 13578 2023-09-08 16:43 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 57861 2025-07-14 11:11 ./usr/include/htslib/hts.h -rw-r--r-- root/root 4617 2025-04-17 08:47 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 11729 2023-08-24 15:40 ./usr/include/htslib/hts_endian.h -rw-r--r-- root/root 5991 2022-07-14 09:33 ./usr/include/htslib/hts_expr.h -rw-r--r-- root/root 3958 2022-05-13 15:25 ./usr/include/htslib/hts_log.h -rw-r--r-- root/root 2842 2022-01-11 12:11 ./usr/include/htslib/hts_os.h -rw-r--r-- root/root 5605 2020-01-23 10:28 ./usr/include/htslib/kbitset.h -rw-r--r-- root/root 2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h -rw-r--r-- root/root 26655 2024-06-20 09:10 ./usr/include/htslib/khash.h -rw-r--r-- root/root 4050 2020-08-10 08:46 ./usr/include/htslib/khash_str2int.h -rw-r--r-- root/root 5189 2023-10-03 15:40 ./usr/include/htslib/klist.h -rw-r--r-- root/root 3733 2022-07-27 10:31 ./usr/include/htslib/knetfile.h -rw-r--r-- root/root 3295 2020-08-27 10:09 ./usr/include/htslib/kroundup.h -rw-r--r-- root/root 9357 2023-10-03 15:40 ./usr/include/htslib/kseq.h -rw-r--r-- root/root 11507 2022-08-16 10:42 ./usr/include/htslib/ksort.h -rw-r--r-- root/root 14148 2025-02-16 23:19 ./usr/include/htslib/kstring.h -rw-r--r-- root/root 8881 2020-07-29 13:09 ./usr/include/htslib/regidx.h -rw-r--r-- root/root 92144 2025-05-28 20:46 ./usr/include/htslib/sam.h -rw-r--r-- root/root 17408 2024-12-20 21:02 ./usr/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root 4992 2024-03-26 10:03 ./usr/include/htslib/tbx.h -rw-r--r-- root/root 12969 2025-01-20 16:14 ./usr/include/htslib/thread_pool.h -rw-r--r-- root/root 68750 2025-03-24 10:41 ./usr/include/htslib/vcf.h -rw-r--r-- root/root 1686 2020-07-11 11:34 ./usr/include/htslib/vcf_sweep.h -rw-r--r-- root/root 4919 2020-09-16 09:17 ./usr/include/htslib/vcfutils.h drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 7201110 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.1.22.1 drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 671 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 2680 2021-04-12 09:37 ./usr/share/doc/libhts-dev/README -rw-r--r-- root/root 2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz -rw-r--r-- root/root 401 2024-04-16 08:41 ./usr/share/doc/libhts-dev/README.test -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/libhts-dev/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/libhts-dev/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/libhts-dev/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 152 2024-11-14 19:27 ./usr/share/lintian/overrides/libhts-dev libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 1351128 bytes: control archive=824 bytes. 570 bytes, 13 lines control 617 bytes, 6 lines md5sums Package: libhts3t64-dbgsym Source: htslib Version: 1.22.1+ds2-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1420 Depends: libhts3t64 (= 1.22.1+ds2-1) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libhts3t64 Build-Ids: 1b470e55db2986890ed6347463a1936764d1fdd3 2b71e863c96319fcbd8537ef9e801ba3e91143fe 5061fb73c04dfde3d859739c02b422288e739274 b45e87a3d5bfbe62ce58383a2c423f1848bc2ee4 bd84982550d7999c3c2e07fcb0ee1de58f7db0a7 drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/1b/ -rw-r--r-- root/root 1288912 2025-09-04 11:56 ./usr/lib/debug/.build-id/1b/470e55db2986890ed6347463a1936764d1fdd3.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/2b/ -rw-r--r-- root/root 15144 2025-09-04 11:56 ./usr/lib/debug/.build-id/2b/71e863c96319fcbd8537ef9e801ba3e91143fe.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/50/ -rw-r--r-- root/root 38976 2025-09-04 11:56 ./usr/lib/debug/.build-id/50/61fb73c04dfde3d859739c02b422288e739274.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/b4/ -rw-r--r-- root/root 54440 2025-09-04 11:56 ./usr/lib/debug/.build-id/b4/5e87a3d5bfbe62ce58383a2c423f1848bc2ee4.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/bd/ -rw-r--r-- root/root 24320 2025-09-04 11:56 ./usr/lib/debug/.build-id/bd/84982550d7999c3c2e07fcb0ee1de58f7db0a7.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 12424 2025-09-04 11:56 ./usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts3t64-dbgsym -> libhts3t64 libhts3t64_1.22.1+ds2-1_amd64.deb --------------------------------- new Debian package, version 2.0. size 475172 bytes: control archive=6172 bytes. 1241 bytes, 24 lines control 883 bytes, 12 lines md5sums 36 bytes, 1 lines shlibs 30767 bytes, 949 lines symbols 66 bytes, 2 lines triggers Package: libhts3t64 Source: htslib Version: 1.22.1+ds2-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1142 Depends: libbz2-1.0, libc6 (>= 2.38), libcurl3t64-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), libssl3t64 (>= 3.0.0), zlib1g (>= 1:1.1.4) Breaks: libhts3 (<< 1.22.1+ds2-1), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~) Replaces: libhts3 Provides: libhts3 (= 1.22.1+ds2-1) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/ -rw-r--r-- root/root 14408 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 34888 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 43080 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 22600 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so -rw-r--r-- root/root 940144 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/libhts.so.3 -> libhts.so.1.22.1 drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts3t64/ -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/libhts3t64/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/libhts3t64/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2025-09-04 11:56 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1537 2025-09-04 11:56 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2025-09-04 11:56 ./usr/share/man/man5/vcf.5.gz drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/man7/ -rw-r--r-- root/root 3418 2025-09-04 11:56 ./usr/share/man/man7/htslib-s3-plugin.7.gz tabix-dbgsym_1.22.1+ds2-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 3127976 bytes: control archive=700 bytes. 456 bytes, 12 lines control 400 bytes, 4 lines md5sums Package: tabix-dbgsym Source: htslib Version: 1.22.1+ds2-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3604 Depends: tabix (= 1.22.1+ds2-1) Section: debug Priority: optional Description: debug symbols for tabix Build-Ids: 0c883c14ebf37faccea93566ac45dd3768872613 41d10903ae44bd6d82cb50c485c48a7725860a5a d89db76efced011f372603cc41d9805728bfbfaf drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/0c/ -rw-r--r-- root/root 1309448 2025-09-04 11:56 ./usr/lib/debug/.build-id/0c/883c14ebf37faccea93566ac45dd3768872613.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/41/ -rw-r--r-- root/root 1011520 2025-09-04 11:56 ./usr/lib/debug/.build-id/41/d10903ae44bd6d82cb50c485c48a7725860a5a.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/d8/ -rw-r--r-- root/root 1273904 2025-09-04 11:56 ./usr/lib/debug/.build-id/d8/9db76efced011f372603cc41d9805728bfbfaf.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 79728 2025-09-04 11:56 ./usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/share/doc/tabix-dbgsym -> tabix tabix_1.22.1+ds2-1_amd64.deb ---------------------------- new Debian package, version 2.0. size 506944 bytes: control archive=1128 bytes. 988 bytes, 20 lines control 545 bytes, 9 lines md5sums Package: tabix Source: htslib Version: 1.22.1+ds2-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2369 Depends: libbz2-1.0, libc6 (>= 2.38), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. . This package is built from the HTSlib source, and provides the bgzip, htsfile, and tabix tools. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/bin/ -rwxr-xr-x root/root 682440 2025-09-04 11:56 ./usr/bin/bgzip -rwxr-xr-x root/root 825768 2025-09-04 11:56 ./usr/bin/htsfile -rwxr-xr-x root/root 846248 2025-09-04 11:56 ./usr/bin/tabix drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/tabix/ -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/tabix/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/man1/ -rw-r--r-- root/root 3064 2025-09-04 11:56 ./usr/share/man/man1/bgzip.1.gz -rw-r--r-- root/root 1919 2025-09-04 11:56 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 3422 2025-09-04 11:56 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 26 Apr 2026 23:35:06 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 26 Apr 2026 23:35:06 +0000 | +------------------------------------------------------------------------------+ Purging /build/htslib-BlqyQO Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 26 Apr 2026 23:35:06 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 100396 Build-Time: 128 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 7 Job: /srv/debomatic/incoming/htslib_1.22.1+ds2-1.dsc Machine Architecture: amd64 Package: htslib Package-Time: 147 Source-Version: 1.22.1+ds2-1 Space: 100396 Status: successful Version: 1.22.1+ds2-1 -------------------------------------------------------------------------------- Finished at 2026-04-26T23:35:04Z Build needed 00:02:27, 100396k disk space