sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | htslib 1.24-2 (amd64) Tue, 22 Sep 2026 07:23:50 +0000 | +==============================================================================+ Package: htslib Version: 1.24-2 Source Version: 1.24-2 Distribution: perl-5.44-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 Tue, 22 Sep 2026 07:23:51 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.24-2 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.24-2 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 22 Sep 2026 07:23:52 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Get:4 file:/srv/reprepro perl-5.44/main amd64 Packages [606 kB] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Tue, 22 Sep 2026 07:23:55 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/htslib_1.24-2.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 22 Sep 2026 07:23:55 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 14), 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 (= 14), 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-P9Y9DS/resolver-8voWEf/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/htslib-P9Y9DS/resolver-8voWEf/apt_archive ./ InRelease Get:2 copy:/build/htslib-P9Y9DS/resolver-8voWEf/apt_archive ./ Release [609 B] Ign:3 copy:/build/htslib-P9Y9DS/resolver-8voWEf/apt_archive ./ Release.gpg Get:4 copy:/build/htslib-P9Y9DS/resolver-8voWEf/apt_archive ./ Sources [726 B] Get:5 copy:/build/htslib-P9Y9DS/resolver-8voWEf/apt_archive ./ Packages [765 B] Fetched 2100 B in 0s (103 kB/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 libcurl4-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 libunistring-dev 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 python3:any python3-requests 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 libcurl4-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 libunistring-dev 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, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 30.7 MB/31.1 MB of archives. After this operation, 117 MB of additional disk space will be used. Get:1 copy:/build/htslib-P9Y9DS/resolver-8voWEf/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B] Get:2 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.14+dfsg-2+b1 [321 kB] 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 1:5.47-4 [345 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-5 [334 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 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 2.42.3-1 [102 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 2.73-2 [516 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 1:1.19-2 [891 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-5 [820 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1+b1 [19.5 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1+b1 [51.2 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.5 [77.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.6.2-3 [552 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 23 [12.7 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 1.15.1-1 [17.1 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.196-1 [61.2 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.4+dfsg-1 [683 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-5 [2704 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 14.5 [944 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 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 1.22.1-3 [335 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-4+b1 [312 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-4+b1 [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 1.17.0-1 [68.1 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.24.0-1 [145 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.70.0-1 [92.7 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.24.0-1 [23.9 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.23.3-1 [61.7 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-6 [253 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.22.0-1 [457 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.26.1-1 [664 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.5-1 [226 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 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 3.8.13-1 [1479 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [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 1.70.0-1 [131 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.17.0-1 [96.3 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.24.0-1 [24.0 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.24.0-1 [204 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.23.3-1 [30.1 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.4-1 [3156 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-6 [402 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-4 [371 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.22.0-1 [590 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.7-1 [102 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.7-1 [3006 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.4-1 [391 kB] Preconfiguring packages ... Fetched 30.7 MB in 0s (86.4 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 15721 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%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_1.0-5_amd64.deb ... Unpacking gettext-base (1.0-5) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b2) ... 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_2.42.3-1_amd64.deb ... Unpacking bsdextrautils (2.42.3-1) ... 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_2.73-2_all.deb ... Unpacking autoconf (2.73-2) ... 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%3a1.19-2_all.deb ... Unpacking automake (1:1.19-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_1.0-5_all.deb ... Unpacking autopoint (1.0-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.4-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.4-1+b1) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.4-1+b1_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.4-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_14.5_all.deb ... Unpacking libdebhelper-perl (14.5) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.6.2-3_all.deb ... Unpacking libtool (2.6.2-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_23_all.deb ... Unpacking dh-autoreconf (23) ... 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_1.15.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.15.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.196-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.196-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.17-1_amd64.deb ... Unpacking dwz (0.17-1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../25-libxml2-16_2.15.4+dfsg-1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.4+dfsg-1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_1.0-5_amd64.deb ... Unpacking gettext (1.0-5) ... 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_14.5_all.deb ... Unpacking debhelper (14.5) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../30-libkrb5support0_1.22.1-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.22.1-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../31-libk5crypto3_1.22.1-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.22.1-3) ... 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_1.22.1-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.22.1-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../34-libgssapi-krb5-2_1.22.1-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.22.1-3) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../35-libgssrpc4t64_1.22.1-3_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.22.1-3) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../36-libkadm5clnt-mit12_1.22.1-3_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.22.1-3) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../37-libkdb5-10t64_1.22.1-3_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.22.1-3) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../38-libkadm5srv-mit12_1.22.1-3_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.22.1-3) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../39-krb5-multidev_1.22.1-3_amd64.deb ... Unpacking krb5-multidev:amd64 (1.22.1-3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../40-libbrotli1_1.2.0-4+b1_amd64.deb ... Unpacking libbrotli1:amd64 (1.2.0-4+b1) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../41-libbrotli-dev_1.2.0-4+b1_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.2.0-4+b1) ... 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_1.17.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.17.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../44-libngtcp2-16_1.24.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.24.0-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../45-libnghttp2-14_1.70.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.70.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../46-libngtcp2-crypto-gnutls8_1.24.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.24.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../47-libpsl5t64_0.23.3-1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.23.3-1) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../48-libssh2-1t64_1.11.1-6_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-6) ... Selecting previously unselected package libcurl4-gnutls:amd64. Preparing to unpack .../49-libcurl4-gnutls_8.22.0-1_amd64.deb ... Unpacking libcurl4-gnutls:amd64 (8.22.0-1) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../50-libevent-2.1-7t64_2.1.13-stable-1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.13-stable-1) ... Selecting previously unselected package libunbound8:amd64. Preparing to unpack .../51-libunbound8_1.26.1-1_amd64.deb ... Unpacking libunbound8:amd64 (1.26.1-1) ... Selecting previously unselected package libgnutls-dane0t64:amd64. Preparing to unpack .../52-libgnutls-dane0t64_3.8.13-1_amd64.deb ... Unpacking libgnutls-dane0t64:amd64 (3.8.13-1) ... Selecting previously unselected package libidn2-dev:amd64. Preparing to unpack .../53-libidn2-dev_2.3.8-5_amd64.deb ... Unpacking libidn2-dev:amd64 (2.3.8-5) ... Selecting previously unselected package libp11-kit-dev:amd64. Preparing to unpack .../54-libp11-kit-dev_0.26.5-1_amd64.deb ... Unpacking libp11-kit-dev:amd64 (0.26.5-1) ... Selecting previously unselected package libtasn1-6-dev:amd64. Preparing to unpack .../55-libtasn1-6-dev_4.21.0-2+b1_amd64.deb ... Unpacking libtasn1-6-dev:amd64 (4.21.0-2+b1) ... 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_3.8.13-1_amd64.deb ... Unpacking libgnutls28-dev:amd64 (3.8.13-1) ... Selecting previously unselected package libkrb5-dev:amd64. Preparing to unpack .../60-libkrb5-dev_1.22.1-3_amd64.deb ... Unpacking libkrb5-dev:amd64 (1.22.1-3) ... Selecting previously unselected package libldap-dev:amd64. Preparing to unpack .../61-libldap-dev_2.6.14+dfsg-2+b1_amd64.deb ... Unpacking libldap-dev:amd64 (2.6.14+dfsg-2+b1) ... 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_1.70.0-1_amd64.deb ... Unpacking libnghttp2-dev:amd64 (1.70.0-1) ... Selecting previously unselected package libnghttp3-dev:amd64. Preparing to unpack .../66-libnghttp3-dev_1.17.0-1_amd64.deb ... Unpacking libnghttp3-dev:amd64 (1.17.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:amd64. Preparing to unpack .../67-libngtcp2-crypto-gnutls-dev_1.24.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:amd64 (1.24.0-1) ... Selecting previously unselected package libngtcp2-dev:amd64. Preparing to unpack .../68-libngtcp2-dev_1.24.0-1_amd64.deb ... Unpacking libngtcp2-dev:amd64 (1.24.0-1) ... Selecting previously unselected package libunistring-dev:amd64. Preparing to unpack .../69-libunistring-dev_1.4.2-1_amd64.deb ... Unpacking libunistring-dev:amd64 (1.4.2-1) ... Selecting previously unselected package libpsl-dev:amd64. Preparing to unpack .../70-libpsl-dev_0.23.3-1_amd64.deb ... Unpacking libpsl-dev:amd64 (0.23.3-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../71-librtmp1_2.6-1_amd64.deb ... Unpacking librtmp1:amd64 (2.6-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../72-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 .../73-librtmp-dev_2.6-1_amd64.deb ... Unpacking librtmp-dev:amd64 (2.6-1) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../74-libssl-dev_3.6.4-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.6.4-1) ... Selecting previously unselected package libssh2-1-dev:amd64. Preparing to unpack .../75-libssh2-1-dev_1.11.1-6_amd64.deb ... Unpacking libssh2-1-dev:amd64 (1.11.1-6) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../76-libzstd-dev_1.5.7+dfsg-4_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.7+dfsg-4) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../77-libcurl4-gnutls-dev_8.22.0-1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.22.0-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../78-libdeflate0_1.25-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.25-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../79-libdeflate-dev_1.25-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.25-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../80-libhtscodecs2_1.6.7-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.7-1) ... Selecting previously unselected package libhtscodecs-dev:amd64. Preparing to unpack .../81-libhtscodecs-dev_1.6.7-1_amd64.deb ... Unpacking libhtscodecs-dev:amd64 (1.6.7-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../82-liblzma-dev_5.8.4-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.4-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../83-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.7-1) ... Setting up libunistring-dev:amd64 (1.4.2-1) ... 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-4) ... Setting up bsdextrautils (2.42.3-1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.4+dfsg-1) ... Setting up libdebhelper-perl (14.5) ... Setting up libbrotli1:amd64 (1.2.0-4+b1) ... Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up libpsl5t64:amd64 (0.23.3-1) ... Setting up libnghttp2-14:amd64 (1.70.0-1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up gettext-base (1.0-5) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.13-stable-1) ... Setting up libcom-err2:amd64 (1.47.4-1+b1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.196-1) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.26.1-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.14+dfsg-2+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1+b1) ... Setting up libssl-dev:amd64 (3.6.4-1) ... Setting up autopoint (1.0-5) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.17.0-1) ... Setting up libnghttp3-dev:amd64 (1.17.0-1) ... Setting up liblzma-dev:amd64 (5.8.4-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.17-1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libngtcp2-16:amd64 (1.24.0-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-6) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up libbrotli-dev:amd64 (1.2.0-4+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.24.0-1) ... Setting up libp11-kit-dev:amd64 (0.26.5-1) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.19-2) ... update-alternatives: using /usr/bin/automake-1.19 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-5) ... 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 (2.6.2-3) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.24.0-1) ... Setting up libngtcp2-dev:amd64 (1.24.0-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.23.3-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (23) ... Setting up libhtscodecs-dev:amd64 (1.6.7-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-6) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.22.0-1) ... Setting up libnghttp2-dev:amd64 (1.70.0-1) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up debhelper (14.5) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.22.0-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.43-6) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 22 Sep 2026 07:24:07 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Tue, 22 Sep 2026 07:24:08 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.47-6 dpkg-dev_1.23.11 g++-15_15.3.0-4 g++-16_16.2.0-3 gcc-15_15.3.0-4 gcc-16_16.2.0-3 libc6-dev_2.43-6 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 linux-libc-dev_7.2.6-1 Package versions: apt_3.3.3 autoconf_2.73-2 automake_1:1.19-2 autopoint_1.0-5 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-4 binutils_2.47-6 binutils-common_2.47-6 binutils-x86-64-linux-gnu_2.47-6 bsdextrautils_2.42.3-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1+b1 coreutils_9.10-1 cpp_4:16.1.0-3 cpp-15_15.3.0-4 cpp-15-x86-64-linux-gnu_15.3.0-4 cpp-16_16.2.0-3 cpp-16-x86-64-linux-gnu_16.2.0-3 cpp-x86-64-linux-gnu_4:16.1.0-3 dash_0.5.12-12 debconf_1.5.92 debhelper_14.5 debian-archive-keyring_2025.1 debianutils_5.24 dh-autoreconf_23 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7+b1 dpkg_1.23.11 dpkg-dev_1.23.11 dwz_0.17-1 eatmydata_131-2 file_1:5.47-4 findutils_4.11.0-2 g++_4:16.1.0-3 g++-15_15.3.0-4 g++-15-x86-64-linux-gnu_15.3.0-4 g++-16_16.2.0-3 g++-16-x86-64-linux-gnu_16.2.0-3 g++-x86-64-linux-gnu_4:16.1.0-3 gcc_4:16.1.0-3 gcc-15_15.3.0-4 gcc-15-base_15.3.0-4 gcc-15-x86-64-linux-gnu_15.3.0-4 gcc-16_16.2.0-3 gcc-16-base_16.2.0-3 gcc-16-x86-64-linux-gnu_16.2.0-3 gcc-x86-64-linux-gnu_4:16.1.0-3 gettext_1.0-5 gettext-base_1.0-5 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7+b1 gpg-agent_2.4.9-7+b1 gpgconf_2.4.9-7+b1 gpgsm_2.4.9-7+b1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.14-1 hostname_3.25 init-system-helpers_1.69+nmu2 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.4.0-1 libapt-pkg7.0_3.3.3 libarchive-zip-perl_1.68-1 libasan8_16.2.0-3 libassuan9_3.0.2-2+b2 libatomic1_16.2.0-3 libattr1_1:2.6.0-1 libaudit-common_1:4.2.1-1 libaudit1_1:4.2.1-1 libbinutils_2.47-6 libblkid1_2.42.3-1 libbrotli-dev_1.2.0-4+b1 libbrotli1_1.2.0-4+b1 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.43-6 libc-dev-bin_2.43-6 libc-gconv-modules-extra_2.43-6 libc6_2.43-6 libc6-dev_2.43-6 libcap-ng0_0.9.6-1 libcc1-0_16.2.0-3 libcom-err2_1.47.4-1+b1 libcrypt1_1:4.5.2+20251210-1 libctf-nobfd0_2.47-6 libctf0_2.47-6 libcurl4-gnutls_8.22.0-1 libcurl4-gnutls-dev_8.22.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.5 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.11 libeatmydata1_131-2+b2 libelf1t64_0.196-1 libevent-2.1-7t64_2.1.13-stable-1 libffi8_3.8.0-2 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-4 libgcc-16-dev_16.2.0-3 libgcc-s1_16.2.0-3 libgcrypt20_1.12.3-2 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_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.2.0-3 libgpg-error0_1.61-5 libgprofng0_2.47-6 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhtscodecs-dev_1.6.7-1 libhtscodecs2_1.6.7-1 libhwasan0_16.2.0-3 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libisl23_0.28-1 libitm1_16.2.0-3 libjansson4_2.15.1-1 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.1-1 libldap-dev_2.6.14+dfsg-2+b1 libldap2_2.6.14+dfsg-2+b1 liblsan0_16.2.0-3 liblz4-1_1.10.0-10 liblzma-dev_5.8.4-1 liblzma5_5.8.4-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.3-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.70.0-1 libnghttp2-dev_1.70.0-1 libnghttp3-9_1.17.0-1 libnghttp3-dev_1.17.0-1 libngtcp2-16_1.24.0-1 libngtcp2-crypto-gnutls-dev_1.24.0-1 libngtcp2-crypto-gnutls8_1.24.0-1 libngtcp2-dev_1.24.0-1 libnpth0t64_1.8-4 libp11-kit-dev_0.26.5-1 libp11-kit0_0.26.5-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.48-3 libperl5.40_5.40.1-8 libperl5.44_5.44.0-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.23.3-1 libpsl5t64_0.23.3-1 libquadmath0_16.2.0-3 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_2.6.1-1+b1 libselinux1_3.11-2 libsframe3_2.47-6 libsmartcols1_2.42.3-1 libsqlite3-0_3.53.4-2 libssh2-1-dev_1.11.1-6 libssh2-1t64_1.11.1-6 libssl-dev_3.6.4-1 libssl3t64_3.6.4-1 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 libsystemd0_262~rc3-1 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.6.2-3 libtsan2_16.2.0-3 libtss2-mu-4.0.1-0t64_4.1.3-7 libtss2-rc0t64_4.1.3-7 libtss2-sys1t64_4.1.3-7 libtss2-tcti-device0t64_4.1.3-7 libtss2-tcti-mssim0t64_4.1.3-7 libtss2-tcti-swtpm0t64_4.1.3-7 libubsan1_16.2.0-3 libuchardet0_0.0.8-2+b2 libudev1_262~rc3-1 libunbound8_1.26.1-1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.3-1 libxml2-16_2.15.4+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-4 libzstd1_1.5.7+dfsg-4 linux-libc-dev_7.2.6-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mount_2.42.3-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.4-1 patch_2.8-2 perl_5.44.0-1 perl-base_5.44.0-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0-1 pinentry-curses_1.3.3-3 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.5.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-6 util-linux_2.42.3-1 xz-utils_5.8.4-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Tue, 22 Sep 2026 07:24:08 +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: 1.24-2 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: 4.7.4 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 (= 14), 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: 17faf63db725c3d9e1bd391753a00b0bb0bc4425 1858118 htslib_1.24.orig.tar.gz 618a53c05091b8e0b055e2c39091f107109576ac 21736 htslib_1.24-2.debian.tar.xz Checksums-Sha256: 19c19ec0ea3fbbf380c79c8c6f465d3a6cc2db3694ab2ff5c3567d468099e5ef 1858118 htslib_1.24.orig.tar.gz 02a97357bdcaaf6b30da68aa6867745e28089566960ba359c6b633d3e7600a3d 21736 htslib_1.24-2.debian.tar.xz Files: 4a36b549462fac72adc758b5ac7c92e6 1858118 htslib_1.24.orig.tar.gz 3508793a742bf78796d4f5033e087767 21736 htslib_1.24-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmqw/4cRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHgtg/9HeCyKY5ci33lM8QgGimSd3YLAWPKJkH8 /hSCzU+3Tbu3eCCkGlFLNhE87Vo8t9d1oxrIVKIkVP8wxQPqlq6lr4tFgmQNvQV0 +eBg8Ltu56ub6Bsyjh9juroibvX6gUzfw/PzA3fMiw0gtg2p/jbFqfYj1nd6bvsl nclgf1SXf/h4o2RGxdFkvd3XraTXkrt3zqzvB4D3wg9mjfZoJfyQyWSMKfcw3B/B TgfFmSmtcIA1wSi1VnNj0i/Md92jQA4B0CDhIdNuz433+U9A9K41hiyFl45IPocp 7OzdmRUKkDYttNDzzYSgg3L/X5z6B8Z2qz7JyC58FL2HZ97ftkNFnyp5E5g2HJ/n 14RLX2UJfdly3XTL0QlplOc9eYiZNGPf1CNWWJuwIXaU0jfEQiqb2phoFsF0HBWW bOXch+KXpIdFOxdJlqsbcg9YLF1XtSfnzUY4IGYGK/Ez7xy+TPkA54rdmbOekdHB xFBJkBgv0hxFKqlwXZGmL65TY/4XblxTwbYkS/WXFQYoW8Ixrgsc5MHOlUeCXr+T C0lmHwMHXm8hrq2S1KTFO+Y5j3VtBHK2ZQ+uwo0WTKgwBApwq7kjq5lJhCOmcYKW D9mCF5HzsVuDcjGnAhOjrHbo3UXiP0fwUMT81lxfrj/ChuAUeBHt7M23iMCv8Zqe Me5BEGK0WaM= =MiwF -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./htslib_1.24-2.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./htslib_1.24-2.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-P9Y9DS/htslib-1.24 dpkg-source: info: unpacking htslib_1.24.orig.tar.gz dpkg-source: info: unpacking htslib_1.24-2.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 Time Build Commands Tue, 22 Sep 2026 07:24:09 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.24-2 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.24-2 perl-5.44-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-P9Y9DS/htslib-1.24 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-24b8878e-82a0-47b1-ac64-c51c0b1adbe3 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 1.24-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from /build/htslib-P9Y9DS/htslib-1.24/debian/source/options: --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-P9Y9DS/htslib-1.24' rm -f test/hfile_libcurl.tmp rm -f libhts.so libhts.so.* 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 -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_alloc 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/test_hfile_libcurl 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-P9Y9DS/htslib-1.24' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' rm -rf test_backup/ make[1]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24/debian/source/options: --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_1.24.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building htslib in ../htslib_1.24-2.debian.tar.xz dpkg-source: info: building htslib in ../htslib_1.24-2.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: no obvious need to run autopoint 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: configure.ac: no need to run autopoint (confirmed) 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: configure.ac: not running make: --make not given 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-P9Y9DS/htslib-1.24' # 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... x86_64-linux-gnu-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 x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 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 x86_64-linux-gnu-gcc options to detect undeclared functions... none needed checking for x86_64-linux-gnu-gcc options to ignore future-version 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 for x86intrin.h... 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_clz... yes checking for working __builtin_prefetch... yes 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 x86_64-linux-gnu-gcc option to support 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 fstatat... yes 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-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.24" \ libdir=/usr/lib/x86_64-linux-gnu make -j2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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=1.24 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 kstring.c: In function ‘boyer_moore’: kstring.c:468:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 faidx.c: In function ‘fai_path’: faidx.c:1067:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 "1.24"' > 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' \ 'x86_64-linux-gnu-gcc' \ '-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 sam.c: In function ‘sam_open_mode_opts’: sam.c:5222:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 vcf.c: In function ‘bcf_get_version’: vcf.c:168:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 cram/cram_decode.c: In function ‘cram_decode_seq’: cram/cram_decode.c:1234:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 cram/cram_io.c: In function ‘refs_load_fai’: cram/cram_io.c:2323:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:5070:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 kstring.c: In function ‘boyer_moore’: kstring.c:468:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 faidx.c: In function ‘fai_path’: faidx.c:1067:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1067 | char *fai_tmp = strstr(fa, HTS_IDX_DELIM); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 hts.c: In function ‘hts_open_format’: hts.c:942:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ hts.c: In function ‘hts_hopen’: hts.c:1478:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ hts.c: In function ‘idx_find_and_load’: hts.c:4929:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 sam.c: In function ‘sam_open_mode_opts’: sam.c:5222:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5222 | if ((opts = strchr(format, ','))) { | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 vcf.c: In function ‘bcf_get_version’: vcf.c:168:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 cram/cram_decode.c: In function ‘cram_decode_seq’: cram/cram_decode.c:1234:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1234 | char *N = memchr(refp, 'N', frag_len); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 cram/cram_io.c: In function ‘refs_load_fai’: cram/cram_io.c:2323:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2323 | char *fn_delim = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ cram/cram_io.c: In function ‘cram_dopen’: cram/cram_io.c:5070:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 5070 | fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename); | ^ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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_alloc.o test/test_alloc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 In file included from test/test_kstring.c:38: test/../kstring.c: In function ‘boyer_moore’: test/../kstring.c:468:24: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 468 | return memchr(str, pat[0], n); | ^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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_hfile_libcurl.o test/test_hfile_libcurl.c In file included from test/test-bcf_set_variant_type.c:30: test/../vcf.c: In function ‘bcf_get_version’: test/../vcf.c:168:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 168 | if (!(major = strstr(version, vcf))) { //bad format | ^ 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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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 hts.c: In function ‘hts_open_format’: hts.c:942:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 942 | char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ hts.c: In function ‘hts_hopen’: hts.c:1478:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1478 | if ((cp = strchr(mode, ','))) { | ^ hts.c: In function ‘idx_find_and_load’: hts.c:4929:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4929 | char *fnidx = strstr(fn, HTS_IDX_DELIM); | ^~~~~~ x86_64-linux-gnu-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 ln -sf libhts.so libhts.so.3 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_alloc test/test_alloc.o x86_64-linux-gnu-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 -lm x86_64-linux-gnu-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 x86_64-linux-gnu-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 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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 -lcurl -lpthread x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_hfile_libcurl test/test_hfile_libcurl.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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-P9Y9DS/htslib-1.24' make[1]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.24" \ 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-P9Y9DS/htslib-1.24=. -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=1.24 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' test/hts_endian test/test_alloc 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" != "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" != "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 -u vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -u 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 -u vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -u vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f vcf_file.tmp.bcf PASS : $tabix vcf_file.tmp.bcf 1:3000151-3000151 PASS : $tabix -u vcf_file.tmp.bcf 1:3000151-3000151 PASS : $tabix vcf_file.tmp.bcf 2:3199812-3199812 PASS : $tabix -u vcf_file.tmp.bcf 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 -u large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p vcf vcf_overlaps.tmp.vcf.gz PASS : $tabix vcf_overlaps.tmp.vcf.gz chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -u vcf_overlaps.tmp.vcf.gz chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.vcf.gz PASS : $tabix -u -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.vcf.gz PASS : $tabix -T vcf_overlaps.tmp.regions vcf_overlaps.tmp.vcf.gz PASS : $tabix -f vcf_overlaps.tmp.bcf PASS : $tabix vcf_overlaps.tmp.bcf chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -u vcf_overlaps.tmp.bcf chr1:1000002-1000002 chr1:1000007-1000007 chr2:1000001-1000001 chr2:1000009-1000009 chr3:1000002-1000002 chr3:1000006-1000006 PASS : $tabix -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.bcf PASS : $tabix -u -R vcf_overlaps.tmp.regions vcf_overlaps.tmp.bcf PASS : $tabix -T vcf_overlaps.tmp.regions vcf_overlaps.tmp.bcf PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -u bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -u bed_file.tbi.tmp.bed.gz Y:100201-100201 Y:100801-100801 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix -u gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix -u gff_file.tbi.tmp.gff.gz X:2935191-2936741 X:2936864-2938094 X:2943200-2945997 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 PASS : $tabix -u vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 43 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 -i fastq_umi=RX UMI.fq 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 PASS : $tview -f -o fastq_rnum -o fastq_umi UMI.sam Expected passes: 43 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) PASS : $test_mod -f 1 MM-variants.sam Expected passes: 17 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tlen && ./tlen.sh tlen.tst Testing CRAM TLEN auto-creation... PASS : $test_view a7.cram PASS : $test_view a7b.cram PASS : $test_view a8.cram PASS : $test_view a8b.cram PASS : $test_view a9.cram PASS : $test_view a9b.cram PASS : $test_view b7.cram PASS : $test_view b7b.cram PASS : $test_view b8.cram PASS : $test_view b8b.cram PASS : $test_view c7.cram PASS : $test_view c7b.cram PASS : $test_view c8.cram PASS : $test_view c8b.cram PASS : $test_view d7.cram PASS : $test_view d7b.cram PASS : $test_view d4.cram PASS : $test_view d4b.cram PASS : $test_view d4c.cram PASS : $test_view d4d.cram PASS : $test_view d4e.cram PASS : $test_view d4f.cram PASS : $test_view d5.cram PASS : $test_view d5b.cram PASS : $test_view d5c.cram PASS : $test_view d5d.cram PASS : $test_view d5e.cram PASS : $test_view d5f.cram PASS : $test_view a4.cram PASS : $test_view a5.cram Expected passes: 30 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" != "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-P9Y9DS/htslib-1.24/test/test_view -l 0 -b -m 14 -x /tmp/5rmjGBMgr_/index.bam.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -b -m 0 -x /tmp/5rmjGBMgr_/index.bam.bai /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -b /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -z -m 14 -x /tmp/5rmjGBMgr_/index.sam.gz.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -z -m 0 -x /tmp/5rmjGBMgr_/index.sam.gz.bai /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -b /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -z -m 14 -x /tmp/5rmjGBMgr_/index.sam.gz.csi /build/htslib-P9Y9DS/htslib-1.24/test/index_dos.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -z -m 0 -x /tmp/5rmjGBMgr_/index.sam.gz.bai /build/htslib-P9Y9DS/htslib-1.24/test/index_dos.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -b /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -C -x /tmp/5rmjGBMgr_/index.cram.crai /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.cram .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index /tmp/5rmjGBMgr_/index.cram .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -p /tmp/5rmjGBMgr_/index3_rgn.sam /tmp/5rmjGBMgr_/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -M -p /tmp/5rmjGBMgr_/index3_rgnm.sam /tmp/5rmjGBMgr_/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -b -m 14 -x /tmp/5rmjGBMgr_/index.bcf.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.vcf > /tmp/5rmjGBMgr_/index.bcf .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.bcf .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -z -m 14 -x /tmp/5rmjGBMgr_/index.vcf.gz.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.vcf > /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -l 0 -z -m 0 -x /tmp/5rmjGBMgr_/index.vcf.gz.tbi /build/htslib-P9Y9DS/htslib-1.24/test/index.vcf > /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -t /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/tabix /tmp/5rmjGBMgr_/index.vcf.gz##idx##/tmp/5rmjGBMgr_/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 2:2000000-2000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -b -m 14 -x /tmp/5rmjGBMgr_/index.bam.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -b -m 0 -x /tmp/5rmjGBMgr_/index.bam.bai /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -b /tmp/5rmjGBMgr_/index.bam .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -z -m 14 -x /tmp/5rmjGBMgr_/index.sam.gz.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -z -m 0 -x /tmp/5rmjGBMgr_/index.sam.gz.bai /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -b /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -z -m 14 -x /tmp/5rmjGBMgr_/index.sam.gz.csi /build/htslib-P9Y9DS/htslib-1.24/test/index_dos.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -z -m 0 -x /tmp/5rmjGBMgr_/index.sam.gz.bai /build/htslib-P9Y9DS/htslib-1.24/test/index_dos.sam > /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -b /tmp/5rmjGBMgr_/index.sam.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -C -x /tmp/5rmjGBMgr_/index.cram.crai /build/htslib-P9Y9DS/htslib-1.24/test/index.sam > /tmp/5rmjGBMgr_/index.cram .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index /tmp/5rmjGBMgr_/index.cram .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -p /tmp/5rmjGBMgr_/index3_rgn.sam /tmp/5rmjGBMgr_/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -M -p /tmp/5rmjGBMgr_/index3_rgnm.sam /tmp/5rmjGBMgr_/index3.cram CHROMOSOME_I:5000-5100 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -b -m 14 -x /tmp/5rmjGBMgr_/index.bcf.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.vcf > /tmp/5rmjGBMgr_/index.bcf .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.bcf .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -z -m 14 -x /tmp/5rmjGBMgr_/index.vcf.gz.csi /build/htslib-P9Y9DS/htslib-1.24/test/index.vcf > /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -c /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -@4 -l 0 -z -m 0 -x /tmp/5rmjGBMgr_/index.vcf.gz.tbi /build/htslib-P9Y9DS/htslib-1.24/test/index.vcf > /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_index -t /tmp/5rmjGBMgr_/index.vcf.gz .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/tabix /tmp/5rmjGBMgr_/index.vcf.gz##idx##/tmp/5rmjGBMgr_/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /tmp/5rmjGBMgr_/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#repeated2.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.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 ./test_view -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam ./test_view -o embed_ref=2 -o no_ref -C -p embed_del.tmp.cram embed_del.sam ./test_view -p embed_del.tmp.cram.sam embed_del.tmp.cram ./compare_sam.pl embed_del.sam embed_del.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-P9Y9DS/htslib-1.24/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 -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_ .. 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_ .. 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_ .. 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_ .. 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_ .. 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_ .. 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 -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_ .. 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_ .. 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#repeated2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam ./test_view -@4 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_ ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./test_view -@4 xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20 ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.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_ .. 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 ./test_view -@4 -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam ./test_view -@4 -p embed_MD.tmp.cram.sam embed_MD.tmp.cram ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam ./test_view -@4 -o embed_ref=2 -o no_ref -C -p embed_del.tmp.cram embed_del.sam ./test_view -@4 -p embed_del.tmp.cram.sam embed_del.tmp.cram ./compare_sam.pl embed_del.sam embed_del.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-P9Y9DS/htslib-1.24/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-P9Y9DS/htslib-1.24/test/test-vcf-api /tmp/5rmjGBMgr_/test-vcf-api.bcf .. ok test_bcf2vcf: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /build/htslib-P9Y9DS/htslib-1.24/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/htslib-P9Y9DS/htslib-1.24/test/test-vcf-sweep /tmp/5rmjGBMgr_/test-vcf-api.bcf .. ok test_vcf_various: /build/htslib-P9Y9DS/htslib-1.24/htsfile -ch /build/htslib-P9Y9DS/htslib-1.24/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/htslib-P9Y9DS/htslib-1.24/htsfile -c /build/htslib-P9Y9DS/htslib-1.24/test/formatcols.vcf .. ok test_vcf_various: /build/htslib-P9Y9DS/htslib-1.24/htsfile -c /build/htslib-P9Y9DS/htslib-1.24/test/noroundtrip.vcf .. ok test_vcf_various: /build/htslib-P9Y9DS/htslib-1.24/htsfile -c /build/htslib-P9Y9DS/htslib-1.24/test/formatmissing.vcf .. ok test_vcf_various: /build/htslib-P9Y9DS/htslib-1.24/htsfile -c /build/htslib-P9Y9DS/htslib-1.24/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/htslib-P9Y9DS/htslib-1.24/test/test_view /build/htslib-P9Y9DS/htslib-1.24/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /build/htslib-P9Y9DS/htslib-1.24/htsfile -c /build/htslib-P9Y9DS/htslib-1.24/test/vcf44_1.vcf .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 74452500 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 34270147 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 11108528 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 42233895 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 8111117 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 85644070 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 49879942 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 47881429 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 69081244 .. ok test-bcf-sr: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr.pl -t /tmp/5rmjGBMgr_ -s 83459376 .. ok test_bcf_sr_no_index: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr --no-index -p all --args /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.b.vcf /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/5rmjGBMgr_/no_index_1.err .. ok test_bcf_sr_no_index: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr --no-index -p all --args /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/5rmjGBMgr_/no_index_2.out 2> /tmp/5rmjGBMgr_/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr --no-index -p all --args /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/5rmjGBMgr_/no_index_3.out 2> /tmp/5rmjGBMgr_/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr --no-index -p all --args /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.rec_order.vcf /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/merge.noidx.a.vcf > /tmp/5rmjGBMgr_/no_index_4.out 2> /tmp/5rmjGBMgr_/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -b -p /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf -x /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf.csi /build/htslib-P9Y9DS/htslib-1.24/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_1.out.vcf -r '1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_2.out.vcf -r '1:1-2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_4.out.vcf -r '1:1-1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_5.out.vcf -r '{1:1}' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/5rmjGBMgr_/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-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_14.out.vcf -t '1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_15.out.vcf -t '1:1-2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_17.out.vcf -t '1:1-1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_18.out.vcf -t '{1:1}' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/5rmjGBMgr_/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf-sr -O vcf -o /tmp/5rmjGBMgr_/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/5rmjGBMgr_/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-P9Y9DS/htslib-1.24/test/test-bcf-translate - .. ok test_convert_padded_header: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -t ce.fa -C /tmp/5rmjGBMgr_/headernul0.bam .. ok test_convert_padded_header: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -t ce.fa -C /tmp/5rmjGBMgr_/headernul1.bam .. ok test_convert_padded_header: /build/htslib-P9Y9DS/htslib-1.24/test/test_view -t ce.fa -C /tmp/5rmjGBMgr_/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/htslib-P9Y9DS/htslib-1.24/bgzip -I /build/htslib-P9Y9DS/htslib-1.24/test/bgziptest.txt.tmp.gz.gzi -c -g /build/htslib-P9Y9DS/htslib-1.24/test/bgziptest.txt .. ok test-logging: /build/htslib-P9Y9DS/htslib-1.24/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/htslib-P9Y9DS/htslib-1.24 /build/htslib-P9Y9DS/htslib-1.24/test/with-shlib.sh /build/htslib-P9Y9DS/htslib-1.24/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -f /build/htslib-P9Y9DS/htslib-1.24/test/realn01.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn01.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -f /build/htslib-P9Y9DS/htslib-1.24/test/realn02.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn02.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -a -f /build/htslib-P9Y9DS/htslib-1.24/test/realn01.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn01.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -a -f /build/htslib-P9Y9DS/htslib-1.24/test/realn02.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn02.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -e -f /build/htslib-P9Y9DS/htslib-1.24/test/realn01.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn01.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -e -f /build/htslib-P9Y9DS/htslib-1.24/test/realn02.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn02.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -r -f /build/htslib-P9Y9DS/htslib-1.24/test/realn02.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn02-r.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -a -f /build/htslib-P9Y9DS/htslib-1.24/test/realn02.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn02_exp.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -f /build/htslib-P9Y9DS/htslib-1.24/test/realn02.fa -i /build/htslib-P9Y9DS/htslib-1.24/test/realn02_exp-a.sam -o - .. ok test_realn: /build/htslib-P9Y9DS/htslib-1.24/test/test_realn -f /build/htslib-P9Y9DS/htslib-1.24/test/realn03.fa -e -i /build/htslib-P9Y9DS/htslib-1.24/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/htslib-P9Y9DS/htslib-1.24/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl,value:overlap,value -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl,value:overlap,value -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl,value:overlap,value -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -O 0.5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -rO 0.5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.1.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.2.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.3.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.3.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.3.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl:overlap -a nbp,frac -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.4.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.4.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.4.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.5.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.5.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.5.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.6.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.6.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.6.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.7.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.7.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.7.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.8.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.8.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.8.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.9.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.9.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.9.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -f smpl -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -x -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -x -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -x -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -f smpl -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -f smpl -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -f smpl -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -x -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -x -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.10.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -m smpl -x -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.12.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.12.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.12.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.12.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.12.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -C 11:11 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.14.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.14.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -C 11:11 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.14.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -C 11:11 -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -C 01:01 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.14.txt -t /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/dst.14.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -C 01:01 -s /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/htslib-P9Y9DS/htslib-1.24/test/annot-tsv/src.14.txt | /build/htslib-P9Y9DS/htslib-1.24/annot-tsv -c 1,2,3 -C 01:01 -t /build/htslib-P9Y9DS/htslib-1.24/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 .. 358 passed .. 358 failed .. 0 if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \ HTS_PATH=. ./test/with-shlib.sh test/test_hfile_libcurl ; \ else \ test/test_hfile_libcurl ; \ fi python3 not found, skipping libcurl retry tests make[2]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' rm -fr -- /tmp/dh-xdg-rundir-BAriCFzy make[1]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/htslib-P9Y9DS/htslib-1.24/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.24" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/htslib-P9Y9DS/htslib-1.24/debian/tmp make -j2 install DESTDIR=/build/htslib-P9Y9DS/htslib-1.24/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-P9Y9DS/htslib-1.24=. -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=1.24 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' mkdir -p -m 755 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/bin /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/include /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/include/htslib /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/share/man/man1 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/share/man/man5 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/share/man/man7 /build/htslib-P9Y9DS/htslib-1.24/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-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.24 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.24#g' htslib.pc.tmp > /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.24 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.24 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 chmod 644 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/htslib-P9Y9DS/htslib-1.24/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-P9Y9DS/htslib-1.24/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-P9Y9DS/htslib-1.24/debian/tmp/usr/share/man/man1 ; \ fi install -p -m 644 faidx.5 sam.5 vcf.5 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/htslib-P9Y9DS/htslib-1.24/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' chmod -R u\+rwX /build/htslib-P9Y9DS/htslib-1.24/debian/tmp # 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-P9Y9DS/htslib-1.24' 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.1.24 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 ./bgzf_internal.h ./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 ./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/embed_MD.sam ./test/embed_del.sam ./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/index3.sam ./test/index3_exp.sam ./test/index_dos.sam ./test/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/mock_http_server.py ./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_alloc.c ./test/test_bgzf.c ./test/test_expr.c ./test/test_faidx.c ./test/test_hfile_libcurl.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/tlen ./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\#repeated2.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-P9Y9DS/htslib-1.24' sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24' # 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-P9Y9DS/htslib-1.24' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' 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-P9Y9DS/htslib-1.24' 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/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 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 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.1.24 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.1.24 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 rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules execute_before_dh_missing make[1]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' # 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-P9Y9DS/htslib-1.24' dh_missing debian/rules override_dh_strip make[1]: Entering directory '/build/htslib-P9Y9DS/htslib-1.24' # 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/66 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.24 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/66/f4e9ba448907acd06021bc7f75c19140f1677c.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/63 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/63/e2bb80173e4b10203cc85ec066ea6baf0340e3.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/63/e2bb80173e4b10203cc85ec066ea6baf0340e3.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/66/f4e9ba448907acd06021bc7f75c19140f1677c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.24 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/66/f4e9ba448907acd06021bc7f75c19140f1677c.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.24 objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/63/e2bb80173e4b10203cc85ec066ea6baf0340e3.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/0d 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/0d/a8051f9c162107d55283c54d6f40b3909b00c8.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/54 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/54/6577d7f0e62f54b97aca609aeb3dfe79721199.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/0d/a8051f9c162107d55283c54d6f40b3909b00c8.debug strip --remove-section=.comment --remove-section=.note 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/0d/a8051f9c162107d55283c54d6f40b3909b00c8.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/cc 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/cc/cef3df476eff8051542255c8bf7b8710ca48a3.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/cc/cef3df476eff8051542255c8bf7b8710ca48a3.debug strip --remove-section=.comment --remove-section=.note 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/cc/cef3df476eff8051542255c8bf7b8710ca48a3.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/78 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/78/0b923bc2245196770f0c2d755d358db3978ec8.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/78/0b923bc2245196770f0c2d755d358db3978ec8.debug strip --remove-section=.comment --remove-section=.note 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/78/0b923bc2245196770f0c2d755d358db3978ec8.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so 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/54/6577d7f0e62f54b97aca609aeb3dfe79721199.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/54/6577d7f0e62f54b97aca609aeb3dfe79721199.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/a5 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/a5/766d24f42d5e46854678ddb0974a356c41cc77.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/a5/766d24f42d5e46854678ddb0974a356c41cc77.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/a5/766d24f42d5e46854678ddb0974a356c41cc77.debug debian/tabix/usr/bin/htsfile 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-P9Y9DS/htslib-1.24' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.24)" >> 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.1.24 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/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars --package=tabix debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars --package=libhts3t64 debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.24 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.so 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/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 -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/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/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 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/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/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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-P9Y9DS/htslib-1.24' find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-P9Y9DS/htslib-1.24' dh_strip_nondeterminism Using 1789983830 as canonical time Normalizing debian/htslib-test/usr/share/htslib-test/test/bgziptest.txt.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/htslib-test/usr/share/htslib-test/test/modhdr.vcf.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 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/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian 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-P9Y9DS/htslib-1.24' cd '/build/htslib-P9Y9DS/htslib-1.24' cd debian/tabix cd debian/libhts-dev 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 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 cd '/build/htslib-P9Y9DS/htslib-1.24' cd '/build/htslib-P9Y9DS/htslib-1.24' 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_computeautosubstvars mv debian/tabix.substvars.new debian/tabix.substvars mv debian/tabix.substvars.new debian/tabix.substvars mv debian/tabix.substvars.new debian/tabix.substvars dh_gencontrol install -m0755 -d debian/libhts3t64/DEBIAN install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64-dbgsym -ldebian/changelog -T/dev/null -cdebian/.debhelper/generated/libhts3t64/rewritten-dctrl -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="0da8051f9c162107d55283c54d6f40b3909b00c8 66f4e9ba448907acd06021bc7f75c19140f1677c 780b923bc2245196770f0c2d755d358db3978ec8 cccef3df476eff8051542255c8bf7b8710ca48a3" -DSection=debug -DMulti-Arch=same -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -cdebian/.debhelper/generated/htslib-test/rewritten-dctrl -Pdebian/htslib-test dpkg-gencontrol: warning: Depends field of package htslib-test: substitution variable ${misc:Depends} used, but is not defined chmod 0644 -- debian/htslib-test/DEBIAN/control install -m0755 -d debian/tabix/DEBIAN install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix-dbgsym -ldebian/changelog -T/dev/null -cdebian/.debhelper/generated/tabix/rewritten-dctrl -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="546577d7f0e62f54b97aca609aeb3dfe79721199 63e2bb80173e4b10203cc85ec066ea6baf0340e3 a5766d24f42d5e46854678ddb0974a356c41cc77" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/.debhelper/generated/libhts3t64/rewritten-dctrl -Pdebian/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/.debhelper/generated/tabix/rewritten-dctrl -Pdebian/tabix dpkg-gencontrol: warning: Pre-Depends field of package libhts3t64: substitution variable ${misc:Pre-Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libhts3t64: substitution variable ${misc:Depends} used, but is not defined chmod 0644 -- debian/libhts3t64/DEBIAN/control install -m0755 -d debian/libhts-dev/DEBIAN dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -cdebian/control -Pdebian/libhts-dev dpkg-gencontrol: warning: Depends field of package tabix: substitution variable ${misc:Depends} used, but is not defined chmod 0644 -- debian/tabix/DEBIAN/control dpkg-gencontrol: warning: Depends field of package libhts-dev: substitution variable ${misc:Depends} used, but is not defined chmod 0644 -- debian/libhts-dev/DEBIAN/control dh_md5sums install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/libhts3t64/DEBIAN cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/htslib-test >/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 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 chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums 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 dh_builddeb dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.24-2_all.deb'. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.24-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.24-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.24-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'tabix' in '../tabix_1.24-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.24-2_amd64.deb'. dpkg-genbuildinfo -O../htslib_1.24-2_amd64.buildinfo dpkg-genchanges -O../htslib_1.24-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from /build/htslib-P9Y9DS/htslib-1.24/debian/source/options: --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-09-22T07:27:35Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 22 Sep 2026 07:27:36 +0000 | +------------------------------------------------------------------------------+ htslib_1.24-2_amd64.changes: ---------------------------- Format: 1.8 Date: Mon, 21 Sep 2026 11:43:50 +0200 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: source all amd64 Version: 1.24-2 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille 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 (1.24-2) unstable; urgency=medium . * Fix autopkgtest Checksums-Sha1: 67f7994956c9265412e10484923c7dc4b02907fe 1520 htslib_1.24-2.dsc 618a53c05091b8e0b055e2c39091f107109576ac 21736 htslib_1.24-2.debian.tar.xz b65ef2328a817695415bd983fc1eef495e3eb651 1249892 htslib-test_1.24-2_all.deb ec9393cf2a3f06a4c6127b87995e0ea476673450 8151 htslib_1.24-2_amd64.buildinfo c357609ef8ae1fa2765ef58d287c47bfef690824 1917060 libhts-dev_1.24-2_amd64.deb a1ca5ed2a709b8b46238747b1f8120c017f96c41 1555148 libhts3t64-dbgsym_1.24-2_amd64.deb 35752868f947f8a0761feb04c837ff2fdb95ff7c 506296 libhts3t64_1.24-2_amd64.deb b4901a9883ff47cda9e3439fe28f87a938dc76b2 3515164 tabix-dbgsym_1.24-2_amd64.deb 5d7ce5ceed98ca8a28144175653aeaa4095340aa 533420 tabix_1.24-2_amd64.deb Checksums-Sha256: e16b27832566f9bef031bb5f9929aff182ff0915f55bbd62f64ed4974f72a237 1520 htslib_1.24-2.dsc 02a97357bdcaaf6b30da68aa6867745e28089566960ba359c6b633d3e7600a3d 21736 htslib_1.24-2.debian.tar.xz be36840a67960c336c77051862cd218994f416d6f7ac36ff1d7a2efc0e687363 1249892 htslib-test_1.24-2_all.deb 4fd8860559486032134455cd6e7b1b87587a390106120384c274672b4c0f66fc 8151 htslib_1.24-2_amd64.buildinfo 594b34a89071756a0cc0000d224399ddaeb49851ab7661194f8fe040050bb743 1917060 libhts-dev_1.24-2_amd64.deb 9605c0935b0b160fa9884fb78a443ec473ffe5917b6ccf3496b886934eca3f59 1555148 libhts3t64-dbgsym_1.24-2_amd64.deb 8b5800faf03174a4555270ead8288c18f29315d2e623b985534f6f6942f595f0 506296 libhts3t64_1.24-2_amd64.deb 775fc135f4c4f953ddf8dec94753e9cdbc64074ade13db7425832694cb4574c7 3515164 tabix-dbgsym_1.24-2_amd64.deb a47e75c7fc4b92dab02d60d3984c85deab3404b5cf4c1c2786d88531897bcdb3 533420 tabix_1.24-2_amd64.deb Files: 30c41209737fdc7a27c5e2194ce349fe 1520 science optional htslib_1.24-2.dsc 3508793a742bf78796d4f5033e087767 21736 science optional htslib_1.24-2.debian.tar.xz 6043cd311449015a8428f2308a67a9c1 1249892 science optional htslib-test_1.24-2_all.deb 8e4651a5a23e84dc486e104d8495ecb8 8151 science optional htslib_1.24-2_amd64.buildinfo f41e580d4a25934fb65fbc6ce67b1404 1917060 libdevel optional libhts-dev_1.24-2_amd64.deb a4cff1a5e7e43cef13bc1640c2c2f6af 1555148 debug optional libhts3t64-dbgsym_1.24-2_amd64.deb af1505f2b1c1107e4771cc9b3e5d6b4f 506296 libs optional libhts3t64_1.24-2_amd64.deb d716ecc98e5da9171f561036d2524a2e 3515164 debug optional tabix-dbgsym_1.24-2_amd64.deb 237fc4525522526176f804b75164f2d4 533420 science optional tabix_1.24-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 22 Sep 2026 07:27:36 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: all amd64 source Version: 1.24-2 Checksums-Md5: 30c41209737fdc7a27c5e2194ce349fe 1520 htslib_1.24-2.dsc 6043cd311449015a8428f2308a67a9c1 1249892 htslib-test_1.24-2_all.deb f41e580d4a25934fb65fbc6ce67b1404 1917060 libhts-dev_1.24-2_amd64.deb a4cff1a5e7e43cef13bc1640c2c2f6af 1555148 libhts3t64-dbgsym_1.24-2_amd64.deb af1505f2b1c1107e4771cc9b3e5d6b4f 506296 libhts3t64_1.24-2_amd64.deb d716ecc98e5da9171f561036d2524a2e 3515164 tabix-dbgsym_1.24-2_amd64.deb 237fc4525522526176f804b75164f2d4 533420 tabix_1.24-2_amd64.deb Checksums-Sha1: 67f7994956c9265412e10484923c7dc4b02907fe 1520 htslib_1.24-2.dsc b65ef2328a817695415bd983fc1eef495e3eb651 1249892 htslib-test_1.24-2_all.deb c357609ef8ae1fa2765ef58d287c47bfef690824 1917060 libhts-dev_1.24-2_amd64.deb a1ca5ed2a709b8b46238747b1f8120c017f96c41 1555148 libhts3t64-dbgsym_1.24-2_amd64.deb 35752868f947f8a0761feb04c837ff2fdb95ff7c 506296 libhts3t64_1.24-2_amd64.deb b4901a9883ff47cda9e3439fe28f87a938dc76b2 3515164 tabix-dbgsym_1.24-2_amd64.deb 5d7ce5ceed98ca8a28144175653aeaa4095340aa 533420 tabix_1.24-2_amd64.deb Checksums-Sha256: e16b27832566f9bef031bb5f9929aff182ff0915f55bbd62f64ed4974f72a237 1520 htslib_1.24-2.dsc be36840a67960c336c77051862cd218994f416d6f7ac36ff1d7a2efc0e687363 1249892 htslib-test_1.24-2_all.deb 594b34a89071756a0cc0000d224399ddaeb49851ab7661194f8fe040050bb743 1917060 libhts-dev_1.24-2_amd64.deb 9605c0935b0b160fa9884fb78a443ec473ffe5917b6ccf3496b886934eca3f59 1555148 libhts3t64-dbgsym_1.24-2_amd64.deb 8b5800faf03174a4555270ead8288c18f29315d2e623b985534f6f6942f595f0 506296 libhts3t64_1.24-2_amd64.deb 775fc135f4c4f953ddf8dec94753e9cdbc64074ade13db7425832694cb4574c7 3515164 tabix-dbgsym_1.24-2_amd64.deb a47e75c7fc4b92dab02d60d3984c85deab3404b5cf4c1c2786d88531897bcdb3 533420 tabix_1.24-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 22 Sep 2026 07:27:35 +0000 Build-Path: /build/htslib-P9Y9DS/htslib-1.24 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.19-2), autopoint (= 1.0-5), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-4), binutils (= 2.47-6), binutils-common (= 2.47-6), binutils-x86-64-linux-gnu (= 2.47-6), bsdextrautils (= 2.42.3-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1+b1), coreutils (= 9.10-1), cpp (= 4:16.1.0-3), cpp-15 (= 15.3.0-4), cpp-15-x86-64-linux-gnu (= 15.3.0-4), cpp-16 (= 16.2.0-3), cpp-16-x86-64-linux-gnu (= 16.2.0-3), cpp-x86-64-linux-gnu (= 4:16.1.0-3), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.5), debianutils (= 5.24), dh-autoreconf (= 23), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.11), dpkg-dev (= 1.23.11), dwz (= 0.17-1), file (= 1:5.47-4), findutils (= 4.11.0-2), g++ (= 4:16.1.0-3), g++-16 (= 16.2.0-3), g++-16-x86-64-linux-gnu (= 16.2.0-3), g++-x86-64-linux-gnu (= 4:16.1.0-3), gcc (= 4:16.1.0-3), gcc-15 (= 15.3.0-4), gcc-15-base (= 15.3.0-4), gcc-15-x86-64-linux-gnu (= 15.3.0-4), gcc-16 (= 16.2.0-3), gcc-16-base (= 16.2.0-3), gcc-16-x86-64-linux-gnu (= 16.2.0-3), gcc-x86-64-linux-gnu (= 4:16.1.0-3), gettext (= 1.0-5), gettext-base (= 1.0-5), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.14-1), hostname (= 3.25), init-system-helpers (= 1.69+nmu2), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.2.0-3), libatomic1 (= 16.2.0-3), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.2.1-1), libaudit1 (= 1:4.2.1-1), libbinutils (= 2.47-6), libblkid1 (= 2.42.3-1), libbrotli-dev (= 1.2.0-4+b1), libbrotli1 (= 1.2.0-4+b1), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.43-6), libc-dev-bin (= 2.43-6), libc-gconv-modules-extra (= 2.43-6), libc6 (= 2.43-6), libc6-dev (= 2.43-6), libcap-ng0 (= 0.9.6-1), libcc1-0 (= 16.2.0-3), libcom-err2 (= 1.47.4-1+b1), libcrypt1 (= 1:4.5.2+20251210-1), libctf-nobfd0 (= 2.47-6), libctf0 (= 2.47-6), libcurl4-gnutls (= 8.22.0-1), libcurl4-gnutls-dev (= 8.22.0-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.5), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.11), libelf1t64 (= 0.196-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libffi8 (= 3.8.0-2), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-4), libgcc-16-dev (= 16.2.0-3), libgcc-s1 (= 16.2.0-3), 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 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.2.0-3), libgprofng0 (= 2.47-6), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhtscodecs-dev (= 1.6.7-1), libhtscodecs2 (= 1.6.7-1), libhwasan0 (= 16.2.0-3), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libisl23 (= 0.28-1), libitm1 (= 16.2.0-3), libjansson4 (= 2.15.1-1), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.14+dfsg-2+b1), libldap2 (= 2.6.14+dfsg-2+b1), liblsan0 (= 16.2.0-3), liblzma-dev (= 5.8.4-1), liblzma5 (= 5.8.4-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.3-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.70.0-1), libnghttp2-dev (= 1.70.0-1), libnghttp3-9 (= 1.17.0-1), libnghttp3-dev (= 1.17.0-1), libngtcp2-16 (= 1.24.0-1), libngtcp2-crypto-gnutls-dev (= 1.24.0-1), libngtcp2-crypto-gnutls8 (= 1.24.0-1), libngtcp2-dev (= 1.24.0-1), libp11-kit-dev (= 0.26.5-1), libp11-kit0 (= 0.26.5-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.48-3), libperl5.44 (= 5.44.0-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.23.3-1), libpsl5t64 (= 0.23.3-1), libquadmath0 (= 16.2.0-3), 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 (= 2.6.1-1+b1), libselinux1 (= 3.11-2), libsframe3 (= 2.47-6), libsmartcols1 (= 2.42.3-1), libssh2-1-dev (= 1.11.1-6), libssh2-1t64 (= 1.11.1-6), libssl-dev (= 3.6.4-1), libssl3t64 (= 3.6.4-1), libstdc++-16-dev (= 16.2.0-3), libstdc++6 (= 16.2.0-3), libsystemd0 (= 262~rc3-1), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.6.2-3), libtsan2 (= 16.2.0-3), libubsan1 (= 16.2.0-3), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 262~rc3-1), libunbound8 (= 1.26.1-1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.3-1), libxml2-16 (= 2.15.4+dfsg-1), libzstd-dev (= 1.5.7+dfsg-4), libzstd1 (= 1.5.7+dfsg-4), linux-libc-dev (= 7.2.6-1), 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+20260608-2), ncurses-bin (= 6.6+20260608-2), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.4-1), patch (= 2.8-2), perl (= 5.44.0-1), perl-base (= 5.44.0-1), perl-modules-5.44 (= 5.44.0-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-6), util-linux (= 2.42.3-1), xz-utils (= 5.8.4-1), 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="1789983830" +------------------------------------------------------------------------------+ | Package contents Tue, 22 Sep 2026 07:27:36 +0000 | +------------------------------------------------------------------------------+ htslib-test_1.24-2_all.deb -------------------------- new Debian package, version 2.0. size 1249892 bytes: control archive=14408 bytes. 969 bytes, 23 lines control 46141 bytes, 593 lines md5sums Package: htslib-test Source: htslib Version: 1.24-2 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 8620 Depends: python3, 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 2026-09-21 09:43 ./ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/htslib-test/ -rw-r--r-- root/root 2560 2026-09-21 09:43 ./usr/share/doc/htslib-test/changelog.Debian.gz -rw-r--r-- root/root 45327 2026-07-09 09:41 ./usr/share/doc/htslib-test/changelog.gz -rw-r--r-- root/root 3951 2026-09-21 09:43 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 1463 2026-09-21 09:43 ./usr/share/doc/libhts-dev/run-unit-test drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/ -rw-r--r-- root/root 55887 2026-09-21 09:43 ./usr/share/htslib-test/Makefile -rw-r--r-- root/root 40939 2026-07-09 09:41 ./usr/share/htslib-test/annot-tsv.c -rw-r--r-- root/root 25602 2026-07-09 09:41 ./usr/share/htslib-test/bcf_sr_sort.c -rw-r--r-- root/root 4239 2026-07-09 09:41 ./usr/share/htslib-test/bcf_sr_sort.h -rw-r--r-- root/root 84324 2026-07-09 09:41 ./usr/share/htslib-test/bgzf.c -rw-r--r-- root/root 2821 2026-07-09 09:41 ./usr/share/htslib-test/bgzf_internal.h -rw-r--r-- root/root 29939 2026-07-09 09:41 ./usr/share/htslib-test/bgzip.c -rw-r--r-- root/root 2487 2026-07-09 09:41 ./usr/share/htslib-test/builddir_vars.mk.in -rw-r--r-- root/root 6550 2026-09-21 09:43 ./usr/share/htslib-test/config.h.in -rw-r--r-- root/root 3847 2026-07-09 09:41 ./usr/share/htslib-test/config.mk.in -rw-r--r-- root/root 34786 2026-07-09 09:41 ./usr/share/htslib-test/configure.ac drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/cram/ -rw-r--r-- root/root 2420 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram.h -rw-r--r-- root/root 74042 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_codecs.c -rw-r--r-- root/root 6659 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_codecs.h -rw-r--r-- root/root 131103 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_decode.c -rw-r--r-- root/root 4568 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_decode.h -rw-r--r-- root/root 148428 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_encode.c -rw-r--r-- root/root 3701 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_encode.h -rw-r--r-- root/root 33325 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_external.c -rw-r--r-- root/root 29910 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_index.c -rw-r--r-- root/root 3866 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_index.h -rw-r--r-- root/root 168808 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_io.c -rw-r--r-- root/root 18393 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_io.h -rw-r--r-- root/root 2911 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_samtools.h -rw-r--r-- root/root 6661 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_stats.c -rw-r--r-- root/root 2273 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_stats.h -rw-r--r-- root/root 29271 2026-07-09 09:41 ./usr/share/htslib-test/cram/cram_structs.h -rw-r--r-- root/root 17233 2026-07-09 09:41 ./usr/share/htslib-test/cram/mFILE.c -rw-r--r-- root/root 3075 2026-07-09 09:41 ./usr/share/htslib-test/cram/mFILE.h -rw-r--r-- root/root 3371 2026-07-09 09:41 ./usr/share/htslib-test/cram/misc.h -rw-r--r-- root/root 14873 2026-07-09 09:41 ./usr/share/htslib-test/cram/open_trace_file.c -rw-r--r-- root/root 5150 2026-07-09 09:41 ./usr/share/htslib-test/cram/open_trace_file.h -rw-r--r-- root/root 6922 2026-09-21 09:43 ./usr/share/htslib-test/cram/os.h -rw-r--r-- root/root 5090 2026-07-09 09:41 ./usr/share/htslib-test/cram/pooled_alloc.c -rw-r--r-- root/root 2185 2026-07-09 09:41 ./usr/share/htslib-test/cram/pooled_alloc.h -rw-r--r-- root/root 4604 2026-07-09 09:41 ./usr/share/htslib-test/cram/string_alloc.c -rw-r--r-- root/root 2356 2026-07-09 09:41 ./usr/share/htslib-test/cram/string_alloc.h -rw-r--r-- root/root 6757 2026-07-09 09:41 ./usr/share/htslib-test/errmod.c -rw-r--r-- root/root 32204 2026-07-09 09:41 ./usr/share/htslib-test/faidx.c -rw-r--r-- root/root 1442 2026-07-09 09:41 ./usr/share/htslib-test/fuzz_settings.h -rw-r--r-- root/root 94233 2026-07-09 09:41 ./usr/share/htslib-test/header.c -rw-r--r-- root/root 11014 2026-07-09 09:41 ./usr/share/htslib-test/header.h -rw-r--r-- root/root 41515 2026-07-09 09:41 ./usr/share/htslib-test/hfile.c -rw-r--r-- root/root 5139 2026-07-09 09:41 ./usr/share/htslib-test/hfile_gcs.c -rw-r--r-- root/root 8046 2026-07-09 09:41 ./usr/share/htslib-test/hfile_internal.h -rw-r--r-- root/root 56166 2026-07-09 09:41 ./usr/share/htslib-test/hfile_libcurl.c -rw-r--r-- root/root 70708 2026-07-09 09:41 ./usr/share/htslib-test/hfile_s3.c -rw-r--r-- root/root 171042 2026-07-09 09:41 ./usr/share/htslib-test/hts.c -rw-r--r-- root/root 28565 2026-07-09 09:41 ./usr/share/htslib-test/hts_expr.c -rw-r--r-- root/root 7671 2026-07-09 09:41 ./usr/share/htslib-test/hts_internal.h -rw-r--r-- root/root 1981 2026-07-09 09:41 ./usr/share/htslib-test/hts_os.c -rw-r--r-- root/root 5886 2026-07-09 09:41 ./usr/share/htslib-test/hts_time_funcs.h lrwxrwxrwx root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/htscodecs.mk -> htscodecs_external.mk -rw-r--r-- root/root 3675 2026-07-09 09:41 ./usr/share/htslib-test/htscodecs_bundled.mk -rw-r--r-- root/root 1710 2026-07-09 09:41 ./usr/share/htslib-test/htscodecs_external.mk -rw-r--r-- root/root 9547 2026-07-09 09:41 ./usr/share/htslib-test/htsfile.c -rw-r--r-- root/root 6943 2026-07-09 09:41 ./usr/share/htslib-test/htslib.mk -rw-r--r-- root/root 484 2026-07-09 09:41 ./usr/share/htslib-test/htslib.pc.in -rw-r--r-- root/root 180 2026-09-21 09:43 ./usr/share/htslib-test/htslib_static.mk -rw-r--r-- root/root 3429 2026-07-09 09:41 ./usr/share/htslib-test/htslib_vars.mk -rw-r--r-- root/root 10879 2026-07-09 09:41 ./usr/share/htslib-test/kfunc.c -rw-r--r-- root/root 14522 2026-07-09 09:41 ./usr/share/htslib-test/kstring.c drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/m4/ -rw-r--r-- root/root 2656 2026-07-09 09:41 ./usr/share/htslib-test/m4/hts_check_compile_flags_needed.m4 -rw-r--r-- root/root 4627 2026-07-09 09:41 ./usr/share/htslib-test/m4/hts_hide_dynamic_syms.m4 -rw-r--r-- root/root 8465 2026-07-09 09:41 ./usr/share/htslib-test/m4/hts_prog_cc_warnings.m4 -rw-r--r-- root/root 10244 2026-07-09 09:41 ./usr/share/htslib-test/m4/pkg.m4 -rw-r--r-- root/root 10656 2026-07-09 09:41 ./usr/share/htslib-test/md5.c -rw-r--r-- root/root 8488 2026-07-09 09:41 ./usr/share/htslib-test/multipart.c drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/os/ -rw-r--r-- root/root 2345 2026-07-09 09:41 ./usr/share/htslib-test/os/lzma_stub.h -rw-r--r-- root/root 2704 2026-07-09 09:41 ./usr/share/htslib-test/os/rand.c -rw-r--r-- root/root 6513 2026-07-09 09:41 ./usr/share/htslib-test/plugin.c -rw-r--r-- root/root 17320 2026-07-09 09:41 ./usr/share/htslib-test/probaln.c -rw-r--r-- root/root 13262 2026-07-09 09:41 ./usr/share/htslib-test/realn.c drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/ref_cache/ -rw-r--r-- root/root 2706 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/cmsg_wrap.c -rw-r--r-- root/root 1384 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/cmsg_wrap.h -rw-r--r-- root/root 21352 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/http_parser.c -rw-r--r-- root/root 3616 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/http_parser.h -rw-r--r-- root/root 7603 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/listener.c -rw-r--r-- root/root 1506 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/listener.h -rw-r--r-- root/root 9864 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/log_files.c -rw-r--r-- root/root 1723 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/log_files.h -rw-r--r-- root/root 35335 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/main.c -rw-r--r-- root/root 2331 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/misc.c -rw-r--r-- root/root 3263 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/misc.h -rw-r--r-- root/root 2940 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/options.h -rw-r--r-- root/root 4032 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/ping.c -rw-r--r-- root/root 1281 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/ping.h -rw-r--r-- root/root 2875 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/poll_wrap.h -rw-r--r-- root/root 3992 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/poll_wrap_epoll.c -rw-r--r-- root/root 7521 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/poll_wrap_poll.c -rw-r--r-- root/root 6061 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/ref_files.c -rw-r--r-- root/root 2361 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/ref_files.h -rw-r--r-- root/root 5655 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/request_handler.c -rw-r--r-- root/root 1595 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/request_handler.h -rw-r--r-- root/root 3112 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/sendfile_wrap.c -rw-r--r-- root/root 1634 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/sendfile_wrap.h -rw-r--r-- root/root 27805 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/server.c -rw-r--r-- root/root 1608 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/server.h -rw-r--r-- root/root 26960 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/transaction.c -rw-r--r-- root/root 3055 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/transaction.h -rw-r--r-- root/root 1588 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/types.h -rw-r--r-- root/root 37250 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/upstream.c -rw-r--r-- root/root 1734 2026-07-09 09:41 ./usr/share/htslib-test/ref_cache/upstream.h -rw-r--r-- root/root 20059 2026-07-09 09:41 ./usr/share/htslib-test/regidx.c -rw-r--r-- root/root 7744 2026-07-09 09:41 ./usr/share/htslib-test/region.c -rw-r--r-- root/root 202174 2026-09-21 09:43 ./usr/share/htslib-test/sam.c -rw-r--r-- root/root 4136 2026-07-09 09:41 ./usr/share/htslib-test/sam_internal.h -rw-r--r-- root/root 26192 2026-07-09 09:41 ./usr/share/htslib-test/sam_mods.c -rw-r--r-- root/root 9146 2026-07-09 09:41 ./usr/share/htslib-test/simd.c -rw-r--r-- root/root 57647 2026-07-09 09:41 ./usr/share/htslib-test/synced_bcf_reader.c -rw-r--r-- root/root 31833 2026-07-09 09:41 ./usr/share/htslib-test/tabix.c -rw-r--r-- root/root 25153 2026-07-09 09:41 ./usr/share/htslib-test/tbx.c drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/test/ drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/ -rw-r--r-- root/root 38 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.1.txt -rw-r--r-- root/root 48 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.10.txt -rw-r--r-- root/root 59 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.11.txt -rw-r--r-- root/root 59 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.12.txt -rw-r--r-- root/root 12 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.14.txt -rw-r--r-- root/root 20 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.2.txt -rw-r--r-- root/root 38 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.3.txt -rw-r--r-- root/root 61 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.4.txt -rw-r--r-- root/root 62 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.5.txt -rw-r--r-- root/root 36 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.6.txt -rw-r--r-- root/root 27 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.7.txt -rw-r--r-- root/root 91 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.8.txt -rw-r--r-- root/root 49 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/dst.9.txt -rw-r--r-- root/root 69 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.1.1.txt -rw-r--r-- root/root 67 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.1.2.txt -rw-r--r-- root/root 88 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.1.3.txt -rw-r--r-- root/root 67 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.1.4.txt -rw-r--r-- root/root 65 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.1.5.txt -rw-r--r-- root/root 67 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.1.6.txt -rw-r--r-- root/root 60 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.10.1.txt -rw-r--r-- root/root 50 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.10.2.txt -rw-r--r-- root/root 40 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.10.3.txt -rw-r--r-- root/root 60 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.10.4.txt -rw-r--r-- root/root 40 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.10.5.txt -rw-r--r-- root/root 50 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.10.6.txt -rw-r--r-- root/root 36 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.11.1.txt -rw-r--r-- root/root 78 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.11.2.txt -rw-r--r-- root/root 63 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.11.3.txt -rw-r--r-- root/root 36 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.12.1.txt -rw-r--r-- root/root 49 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.13.1.txt -rw-r--r-- root/root 38 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.13.2.txt -rw-r--r-- root/root 43 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.13.3.txt -rw-r--r-- root/root 44 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.13.4.txt -rw-r--r-- root/root 12 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.14.1.txt -rw-r--r-- root/root 6 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.14.2.txt -rw-r--r-- root/root 28 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.2.1.txt -rw-r--r-- root/root 26 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.2.2.txt -rw-r--r-- root/root 38 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.2.3.txt -rw-r--r-- root/root 38 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.2.4.txt -rw-r--r-- root/root 46 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.2.5.txt -rw-r--r-- root/root 26 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.2.6.txt -rw-r--r-- root/root 97 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.3.1.txt -rw-r--r-- root/root 87 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.4.1.txt -rw-r--r-- root/root 95 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.5.1.txt -rw-r--r-- root/root 48 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.6.1.txt -rw-r--r-- root/root 42 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.7.1.txt -rw-r--r-- root/root 135 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.8.1.txt -rw-r--r-- root/root 111 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/out.9.1.txt -rw-r--r-- root/root 58 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.1.txt -rw-r--r-- root/root 38 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.10.txt -rw-r--r-- root/root 75 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.11.txt -rw-r--r-- root/root 75 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.12.txt -rw-r--r-- root/root 27 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.13.txt -rw-r--r-- root/root 12 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.14.txt -rw-r--r-- root/root 40 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.2.txt -rw-r--r-- root/root 58 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.3.txt -rw-r--r-- root/root 73 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.4.txt -rw-r--r-- root/root 62 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.5.txt -rw-r--r-- root/root 18 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.6.txt -rw-r--r-- root/root 18 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.7.txt -rw-r--r-- root/root 94 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.8.txt -rw-r--r-- root/root 36 2026-07-09 09:41 ./usr/share/htslib-test/test/annot-tsv/src.9.txt -rw-r--r-- root/root 751 2026-07-09 09:41 ./usr/share/htslib-test/test/auxf#values.sam -rw-r--r-- root/root 5152 2026-07-09 09:41 ./usr/share/htslib-test/test/auxf#values_java.cram -rw-r--r-- root/root 29 2026-07-09 09:41 ./usr/share/htslib-test/test/auxf.fa -rw-r--r-- root/root 18 2026-07-09 09:41 ./usr/share/htslib-test/test/auxf.fa.fai drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/ -rw-r--r-- root/root 739 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-MNf1.sam -rw-r--r-- root/root 739 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-MNf2.sam -rw-r--r-- root/root 739 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-MNp.sam -rw-r--r-- root/root 193 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-bounds+.sam -rw-r--r-- root/root 195 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-bounds-.sam -rw-r--r-- root/root 372 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-chebi.out -rw-r--r-- root/root 172 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-chebi.sam -rw-r--r-- root/root 343 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-double.out -rw-r--r-- root/root 254 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-double.sam -rw-r--r-- root/root 924 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-explicit-f.out -rw-r--r-- root/root 791 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-explicit-x.out -rw-r--r-- root/root 768 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-explicit.out -rw-r--r-- root/root 1083 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-explicit.sam -rw-r--r-- root/root 765 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-multi.out -rw-r--r-- root/root 537 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-multi.sam -rw-r--r-- root/root 1096 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-not-all-modded.out -rw-r--r-- root/root 558 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-not-all-modded.sam -rw-r--r-- root/root 510 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-orient.sam -rw-r--r-- root/root 713 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-pileup.out -rw-r--r-- root/root 723 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-pileup.sam -rw-r--r-- root/root 518 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-pileup2.out -rw-r--r-- root/root 372 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-pileup2.sam -rw-r--r-- root/root 676 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-variants.out -rw-r--r-- root/root 660 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/MM-variants.sam -rwxr-xr-x root/root 1331 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/base-mods.sh -rw-r--r-- root/root 2849 2026-07-09 09:41 ./usr/share/htslib-test/test/base_mods/base-mods.tst drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/ -rw-r--r-- root/root 518 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.a.vcf -rw-r--r-- root/root 128 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.abc.expected.out -rw-r--r-- root/root 634 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.b.vcf -rw-r--r-- root/root 634 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.c.vcf -rw-r--r-- root/root 518 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.hdr_order.vcf -rw-r--r-- root/root 518 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/merge.noidx.rec_order.vcf -rw-r--r-- root/root 217 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.1.out -rw-r--r-- root/root 201 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.2.out -rw-r--r-- root/root 221 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.3.out -rw-r--r-- root/root 203 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.4.out -rw-r--r-- root/root 225 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.5.out -rw-r--r-- root/root 205 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.6.out -rw-r--r-- root/root 241 2026-07-09 09:41 ./usr/share/htslib-test/test/bcf-sr/weird-chr-names.vcf drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/bgzf_boundaries/ -rw-r--r-- root/root 432 2026-07-09 09:41 ./usr/share/htslib-test/test/bgzf_boundaries/bgzf_boundaries1.bam -rw-r--r-- root/root 432 2026-07-09 09:41 ./usr/share/htslib-test/test/bgzf_boundaries/bgzf_boundaries2.bam -rw-r--r-- root/root 897 2026-07-09 09:41 ./usr/share/htslib-test/test/bgzf_boundaries/bgzf_boundaries3.bam -rw-r--r-- root/root 15 2026-07-09 09:41 ./usr/share/htslib-test/test/bgziptest.txt -rw-r--r-- root/root 181 2026-09-21 09:43 ./usr/share/htslib-test/test/bgziptest.txt.gz -rw-r--r-- root/root 88 2026-07-09 09:41 ./usr/share/htslib-test/test/bgziptest.txt.gz.gzi -rw-r--r-- root/root 148 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#bounds.sam -rw-r--r-- root/root 337 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#clip.sam -rw-r--r-- root/root 433 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#noseq.sam -rw-r--r-- root/root 388 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#pad1.sam -rw-r--r-- root/root 527 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#pad2.sam -rw-r--r-- root/root 665 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#pad3.sam -rw-r--r-- root/root 429 2026-07-09 09:41 ./usr/share/htslib-test/test/c1#unknown.sam -rw-r--r-- root/root 15 2026-07-09 09:41 ./usr/share/htslib-test/test/c1.fa -rw-r--r-- root/root 14 2026-07-09 09:41 ./usr/share/htslib-test/test/c1.fa.fai -rw-r--r-- root/root 847 2026-07-09 09:41 ./usr/share/htslib-test/test/c2#pad.sam -rw-r--r-- root/root 14 2026-07-09 09:41 ./usr/share/htslib-test/test/c2.fa -rw-r--r-- root/root 12 2026-07-09 09:41 ./usr/share/htslib-test/test/c2.fa.fai -rw-r--r-- root/root 341 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#1.sam -rw-r--r-- root/root 322632 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#1000.sam -rw-r--r-- root/root 645 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#2.sam -rw-r--r-- root/root 1872 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#5.sam -rw-r--r-- root/root 1836 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#5b.sam -rw-r--r-- root/root 6784 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#5b_java.cram -rw-r--r-- root/root 2147244 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#large_seq.sam -rw-r--r-- root/root 547 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#supp.sam -rw-r--r-- root/root 1638 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#tag_depadded.sam -rw-r--r-- root/root 1650 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#tag_padded.sam -rw-r--r-- root/root 1325 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#unmap.sam -rw-r--r-- root/root 2747 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#unmap1.sam -rw-r--r-- root/root 5525 2026-07-09 09:41 ./usr/share/htslib-test/test/ce#unmap2.sam -rw-r--r-- root/root 1060702 2026-07-09 09:41 ./usr/share/htslib-test/test/ce.fa -rw-r--r-- root/root 230 2026-07-09 09:41 ./usr/share/htslib-test/test/ce.fa.fai -rw-r--r-- root/root 268 2026-07-09 09:41 ./usr/share/htslib-test/test/colons.bam -rw-r--r-- root/root 424 2026-07-09 09:41 ./usr/share/htslib-test/test/colons.bam.bai -rwxr-xr-x root/root 6549 2026-09-21 09:43 ./usr/share/htslib-test/test/compare_sam.pl -rwxr-xr-x root/root 4307 2026-07-09 09:41 ./usr/share/htslib-test/test/cross_validate.sh -rw-r--r-- root/root 288 2026-07-09 09:41 ./usr/share/htslib-test/test/embed_MD.sam -rw-r--r-- root/root 50 2026-07-09 09:41 ./usr/share/htslib-test/test/embed_del.sam -rw-r--r-- root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/emptyfile drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/ -rw-r--r-- root/root 326 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/ce.1.expected.fa -rw-r--r-- root/root 94 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/faidx.1.expected.fa -rw-r--r-- root/root 289 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/faidx.fa -rw-r--r-- root/root 117 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/faidx.fa.expected.fai -rw-r--r-- root/root 4437 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/faidx.tst -rw-r--r-- root/root 336 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/fastqs.1.expected.fq -rw-r--r-- root/root 225 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/fastqs.2.expected.fa -rw-r--r-- root/root 48599 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/fastqs.fq -rw-r--r-- root/root 3750 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/fastqs.fq.expected.fai -rwxr-xr-x root/root 1314 2026-07-09 09:41 ./usr/share/htslib-test/test/faidx/test-faidx.sh drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/ -rw-r--r-- root/root 1025 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/UMI.fq -rw-r--r-- root/root 1144 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/UMI.sam -rw-r--r-- root/root 4675 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/fastq.tst -rw-r--r-- root/root 667 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/filter_casava-q.sam -rw-r--r-- root/root 596 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/filter_casava.fa -rw-r--r-- root/root 1008 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/filter_casava.fq -rw-r--r-- root/root 1063 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/filter_casava.sam -rw-r--r-- root/root 1765 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_aux-q.sam -rw-r--r-- root/root 2755 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_aux.sam -rw-r--r-- root/root 1665 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_casava-q.sam -rw-r--r-- root/root 2655 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_casava.sam -rw-r--r-- root/root 1665 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_casavaOX-q.sam -rw-r--r-- root/root 2655 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_casavaOX.sam -rw-r--r-- root/root 1525 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_noaux-q.sam -rw-r--r-- root/root 2515 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/inter_noaux.sam -rw-r--r-- root/root 1600 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/interleaved.fa -rw-r--r-- root/root 2630 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/interleaved.fq -rw-r--r-- root/root 1490 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/interleaved_casava.fa -rw-r--r-- root/root 2520 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/interleaved_casava.fq -rw-r--r-- root/root 1052 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/longline.fq -rw-r--r-- root/root 1065 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/longline.sam -rw-r--r-- root/root 22 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/minimal-q.sam -rw-r--r-- root/root 5 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/minimal.fa -rw-r--r-- root/root 9 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/minimal.fq -rw-r--r-- root/root 22 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/minimal.sam -rw-r--r-- root/root 126 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/multiline-q.sam -rw-r--r-- root/root 98 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/multiline.fa -rw-r--r-- root/root 188 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/multiline.fq -rw-r--r-- root/root 202 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/multiline.sam -rw-r--r-- root/root 512 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/name2-q.sam -rw-r--r-- root/root 482 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/name2.fa -rw-r--r-- root/root 894 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/name2.fq -rw-r--r-- root/root 908 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/name2.sam -rw-r--r-- root/root 950 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r1-q.sam -rw-r--r-- root/root 870 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r1.fa -rw-r--r-- root/root 1385 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r1.fq -rw-r--r-- root/root 1445 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r1.sam -rw-r--r-- root/root 815 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r2-q.sam -rw-r--r-- root/root 730 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r2.fa -rw-r--r-- root/root 1245 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r2.fq -rw-r--r-- root/root 1310 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/r2.sam -rw-r--r-- root/root 720 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/single.fa -rw-r--r-- root/root 1235 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/single.fq -rw-r--r-- root/root 805 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/single_aux-q.sam -rw-r--r-- root/root 1300 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/single_aux.sam -rw-r--r-- root/root 755 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/single_noaux-q.sam -rw-r--r-- root/root 1250 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/single_noaux.sam -rwxr-xr-x root/root 1318 2026-07-09 09:41 ./usr/share/htslib-test/test/fastq/test-fastq.sh -rw-r--r-- root/root 4951 2026-07-09 09:41 ./usr/share/htslib-test/test/fastqs_README.txt -rw-r--r-- root/root 2438 2026-07-09 09:41 ./usr/share/htslib-test/test/fieldarith.c -rw-r--r-- root/root 910 2026-07-09 09:41 ./usr/share/htslib-test/test/fieldarith.sam -rw-r--r-- root/root 241 2026-07-09 09:41 ./usr/share/htslib-test/test/formatcols.vcf -rw-r--r-- root/root 226 2026-07-09 09:41 ./usr/share/htslib-test/test/formatmissing-out.vcf -rw-r--r-- root/root 226 2026-07-09 09:41 ./usr/share/htslib-test/test/formatmissing.vcf drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/test/fuzz/ -rw-r--r-- root/root 5618 2026-09-21 09:43 ./usr/share/htslib-test/test/fuzz/hts_open_fuzzer.c -rwxr-xr-x root/root 3581 2026-09-21 09:43 ./usr/share/htslib-test/test/header_syms.pl -rw-r--r-- root/root 12062 2026-07-09 09:41 ./usr/share/htslib-test/test/hfile.c -rw-r--r-- root/root 17620 2026-07-09 09:41 ./usr/share/htslib-test/test/hts_endian.c -rw-r--r-- root/root 776 2026-07-09 09:41 ./usr/share/htslib-test/test/index.bam.bai -rw-r--r-- root/root 130 2026-07-09 09:41 ./usr/share/htslib-test/test/index.bam.csi -rw-r--r-- root/root 144 2026-07-09 09:41 ./usr/share/htslib-test/test/index.bcf.csi -rw-r--r-- root/root 83 2026-07-09 09:41 ./usr/share/htslib-test/test/index.cram.crai -rw-r--r-- root/root 54185 2026-07-09 09:41 ./usr/share/htslib-test/test/index.sam -rw-r--r-- root/root 776 2026-07-09 09:41 ./usr/share/htslib-test/test/index.sam.gz.bai -rw-r--r-- root/root 130 2026-07-09 09:41 ./usr/share/htslib-test/test/index.sam.gz.csi -rw-r--r-- root/root 68888 2026-07-09 09:41 ./usr/share/htslib-test/test/index.vcf -rw-r--r-- root/root 168 2026-07-09 09:41 ./usr/share/htslib-test/test/index.vcf.gz.csi -rw-r--r-- root/root 206 2026-07-09 09:41 ./usr/share/htslib-test/test/index.vcf.gz.tbi -rw-r--r-- root/root 477 2026-07-09 09:41 ./usr/share/htslib-test/test/index2.sam -rw-r--r-- root/root 786 2026-07-09 09:41 ./usr/share/htslib-test/test/index3.sam -rw-r--r-- root/root 442 2026-07-09 09:41 ./usr/share/htslib-test/test/index3_exp.sam -rw-r--r-- root/root 54375 2026-07-09 09:41 ./usr/share/htslib-test/test/index_dos.sam drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/ -rw-r--r-- root/root 594 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/index.expected1.vcf -rw-r--r-- root/root 83 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/index.expected2.vcf -rw-r--r-- root/root 21491 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/index.vcf -rw-r--r-- root/root 31717 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/longref.sam -rw-r--r-- root/root 8300 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/longref_itr.expected.sam -rw-r--r-- root/root 15015 2026-07-09 09:41 ./usr/share/htslib-test/test/longrefs/longref_multi.expected.sam drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/htslib-test/test/maintainer/ -rwxr-xr-x root/root 3292 2026-09-21 09:43 ./usr/share/htslib-test/test/maintainer/check_copyright.pl -rwxr-xr-x root/root 2734 2026-09-21 09:43 ./usr/share/htslib-test/test/maintainer/check_spaces.pl -rw-r--r-- root/root 1017 2026-07-09 09:41 ./usr/share/htslib-test/test/md#1.sam -rw-r--r-- root/root 45 2026-07-09 09:41 ./usr/share/htslib-test/test/md.fa -rw-r--r-- root/root 13 2026-07-09 09:41 ./usr/share/htslib-test/test/md.fa.fai -rwxr-xr-x root/root 7815 2026-07-09 09:41 ./usr/share/htslib-test/test/mock_http_server.py -rw-r--r-- root/root 148 2026-07-09 09:41 ./usr/share/htslib-test/test/modhdr.expected.vcf -rw-r--r-- root/root 156 2026-09-21 09:43 ./usr/share/htslib-test/test/modhdr.vcf.gz -rw-r--r-- root/root 86 2026-07-09 09:41 ./usr/share/htslib-test/test/modhdr.vcf.gz.csi drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/ -rw-r--r-- root/root 374 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/c1#pad1.out -rw-r--r-- root/root 2024 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/c1#pad1.sam -rw-r--r-- root/root 486 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/c1#pad2.out -rw-r--r-- root/root 2311 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/c1#pad2.sam -rw-r--r-- root/root 194 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/c1#pad3.out -rw-r--r-- root/root 2393 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/c1#pad3.sam -rw-r--r-- root/root 174 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_D.out -rw-r--r-- root/root 1534 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_D.sam -rw-r--r-- root/root 261 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_DI.out -rw-r--r-- root/root 1747 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_DI.sam -rw-r--r-- root/root 179 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_I.out -rw-r--r-- root/root 1821 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_I.sam -rw-r--r-- root/root 241 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_ID.out -rw-r--r-- root/root 1958 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_ID.sam -rw-r--r-- root/root 166 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_N.out -rw-r--r-- root/root 1739 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_N.sam -rw-r--r-- root/root 366 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_N2.out -rw-r--r-- root/root 2152 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_N2.sam -rw-r--r-- root/root 229 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_P.out -rw-r--r-- root/root 1796 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_P.sam -rw-r--r-- root/root 214 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_overlap1.out -rw-r--r-- root/root 149 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_overlap1.sam -rw-r--r-- root/root 214 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_overlap2.out -rw-r--r-- root/root 149 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mp_overlap2.sam -rw-r--r-- root/root 2725 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/mpileup.tst -rw-r--r-- root/root 1294 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/small.bam -rw-r--r-- root/root 4171 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/small.out -rwxr-xr-x root/root 1295 2026-07-09 09:41 ./usr/share/htslib-test/test/mpileup/test-pileup.sh -rw-r--r-- root/root 1691 2026-07-09 09:41 ./usr/share/htslib-test/test/no_hdr_sq_1.bam -rw-r--r-- root/root 94 2026-07-09 09:41 ./usr/share/htslib-test/test/no_hdr_sq_1.bam.csi -rw-r--r-- root/root 2019 2026-07-09 09:41 ./usr/share/htslib-test/test/no_hdr_sq_1.expected.sam -rw-r--r-- root/root 404 2026-07-09 09:41 ./usr/share/htslib-test/test/noroundtrip-out.vcf -rw-r--r-- root/root 367 2026-07-09 09:41 ./usr/share/htslib-test/test/noroundtrip.vcf -rw-r--r-- root/root 7459 2026-07-09 09:41 ./usr/share/htslib-test/test/pileup.c -rw-r--r-- root/root 7161 2026-07-09 09:41 ./usr/share/htslib-test/test/pileup_mod.c -rw-r--r-- root/root 5076 2026-07-09 09:41 ./usr/share/htslib-test/test/plugins-dlhts.c -rw-r--r-- root/root 13337 2026-07-09 09:41 ./usr/share/htslib-test/test/range.bam -rw-r--r-- root/root 360 2026-07-09 09:41 ./usr/share/htslib-test/test/range.bam.bai -rw-r--r-- root/root 11182 2026-07-09 09:41 ./usr/share/htslib-test/test/range.cram -rw-r--r-- root/root 94 2026-07-09 09:41 ./usr/share/htslib-test/test/range.cram.crai -rw-r--r-- root/root 3496 2026-07-09 09:41 ./usr/share/htslib-test/test/range.out -rw-r--r-- root/root 4833 2026-07-09 09:41 ./usr/share/htslib-test/test/range.out2 -rw-r--r-- root/root 719 2026-07-09 09:41 ./usr/share/htslib-test/test/realn01.fa -rw-r--r-- root/root 21 2026-07-09 09:41 ./usr/share/htslib-test/test/realn01.fa.fai -rw-r--r-- root/root 1843 2026-07-09 09:41 ./usr/share/htslib-test/test/realn01.sam -rw-r--r-- root/root 2157 2026-07-09 09:41 ./usr/share/htslib-test/test/realn01_exp-a.sam -rw-r--r-- root/root 2157 2026-07-09 09:41 ./usr/share/htslib-test/test/realn01_exp-e.sam -rw-r--r-- root/root 2157 2026-07-09 09:41 ./usr/share/htslib-test/test/realn01_exp.sam -rw-r--r-- root/root 3758 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02-r.sam -rw-r--r-- root/root 4284 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02.fa -rw-r--r-- root/root 17 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02.fa.fai -rw-r--r-- root/root 2894 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02.sam -rw-r--r-- root/root 3758 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02_exp-a.sam -rw-r--r-- root/root 3758 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02_exp-e.sam -rw-r--r-- root/root 3758 2026-07-09 09:41 ./usr/share/htslib-test/test/realn02_exp.sam -rw-r--r-- root/root 16 2026-07-09 09:41 ./usr/share/htslib-test/test/realn03.fa -rw-r--r-- root/root 14 2026-07-09 09:41 ./usr/share/htslib-test/test/realn03.fa.fai -rw-r--r-- root/root 138 2026-07-09 09:41 ./usr/share/htslib-test/test/realn03.sam -rw-r--r-- root/root 172 2026-07-09 09:41 ./usr/share/htslib-test/test/realn03_exp.sam drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/ref_cache/ -rw-r--r-- root/root 2016 2026-07-09 09:41 ./usr/share/htslib-test/test/ref_cache/ce_m5.sam -rw-r--r-- root/root 84621 2026-07-09 09:41 ./usr/share/htslib-test/test/sam.c drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/ -rwxr-xr-x root/root 1291 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/filter.sh -rw-r--r-- root/root 2927 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/filter.tst -rw-r--r-- root/root 2 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func1.out -rw-r--r-- root/root 3 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func2.out -rw-r--r-- root/root 2 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func3.out -rw-r--r-- root/root 4 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func4.out -rw-r--r-- root/root 1552 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func5.out -rw-r--r-- root/root 585 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func6.out -rw-r--r-- root/root 946 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func7.out -rw-r--r-- root/root 40 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/func8.out -rw-r--r-- root/root 3 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/int1.out -rw-r--r-- root/root 3 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/int2.out -rw-r--r-- root/root 3 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/int3.out -rw-r--r-- root/root 485 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string1.out -rw-r--r-- root/root 451 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string2.out -rw-r--r-- root/root 748 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string3.out -rw-r--r-- root/root 1136 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string4.out -rw-r--r-- root/root 498 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string5.out -rw-r--r-- root/root 319 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string6.out -rw-r--r-- root/root 410 2026-07-09 09:41 ./usr/share/htslib-test/test/sam_filter/string7.out -rwxr-xr-x root/root 5728 2026-07-09 09:41 ./usr/share/htslib-test/test/simple_test_driver.sh -rw-r--r-- root/root 98 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix.out drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/ -rw-r--r-- root/root 47 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/bed_file.Y.100200.out -rw-r--r-- root/root 1857 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/bed_file.bed -rw-r--r-- root/root 407 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/bed_file.separate.out -rw-r--r-- root/root 141 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/bed_file.unique.out -rw-r--r-- root/root 405 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/gff_file.X.2934832.2935190.out -rw-r--r-- root/root 5618 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/gff_file.gff -rw-r--r-- root/root 475 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/gff_file.unique.out -rw-r--r-- root/root 288 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/large_chr.20.1.2147483647.out -rw-r--r-- root/root 622 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/large_chr.vcf -rw-r--r-- root/root 6140 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/tabix.tst -rwxr-xr-x root/root 1312 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/test-tabix.sh -rw-r--r-- root/root 67 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_file.1.3000151.out -rw-r--r-- root/root 74 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_file.2.3199812.out -rw-r--r-- root/root 4485 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_file.bcf -rw-r--r-- root/root 4302 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_file.vcf -rw-r--r-- root/root 1120 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_overlaps.bcf -rw-r--r-- root/root 518 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_overlaps.no_u.out -rw-r--r-- root/root 398 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_overlaps.unique.out -rw-r--r-- root/root 934 2026-07-09 09:41 ./usr/share/htslib-test/test/tabix/vcf_overlaps.vcf -rw-r--r-- root/root 10983 2026-07-09 09:41 ./usr/share/htslib-test/test/test-bcf-sr.c -rwxr-xr-x root/root 17395 2026-09-21 09:43 ./usr/share/htslib-test/test/test-bcf-sr.pl -rw-r--r-- root/root 8997 2026-07-09 09:41 ./usr/share/htslib-test/test/test-bcf-translate.c -rw-r--r-- root/root 869 2026-07-09 09:41 ./usr/share/htslib-test/test/test-bcf-translate.out -rw-r--r-- root/root 4362 2026-07-09 09:41 ./usr/share/htslib-test/test/test-bcf_set_variant_type.c -rwxr-xr-x root/root 2601 2026-09-21 09:43 ./usr/share/htslib-test/test/test-logging.pl -rw-r--r-- root/root 7064 2026-07-09 09:41 ./usr/share/htslib-test/test/test-parse-reg.c -rw-r--r-- root/root 16999 2026-07-09 09:41 ./usr/share/htslib-test/test/test-regidx.c -rw-r--r-- root/root 48160 2026-07-09 09:41 ./usr/share/htslib-test/test/test-vcf-api.c -rw-r--r-- root/root 2064 2026-07-09 09:41 ./usr/share/htslib-test/test/test-vcf-api.out -rw-r--r-- root/root 2024 2026-07-09 09:41 ./usr/share/htslib-test/test/test-vcf-hdr-in.vcf -rw-r--r-- root/root 1349 2026-07-09 09:41 ./usr/share/htslib-test/test/test-vcf-hdr.out -rw-r--r-- root/root 3840 2026-07-09 09:41 ./usr/share/htslib-test/test/test-vcf-sweep.c -rw-r--r-- root/root 92 2026-07-09 09:41 ./usr/share/htslib-test/test/test-vcf-sweep.out -rwxr-xr-x root/root 68819 2026-09-21 09:43 ./usr/share/htslib-test/test/test.pl -rw-r--r-- root/root 12017 2026-07-09 09:41 ./usr/share/htslib-test/test/test_alloc.c -rw-r--r-- root/root 36977 2026-07-09 09:41 ./usr/share/htslib-test/test/test_bgzf.c -rw-r--r-- root/root 12549 2026-07-09 09:41 ./usr/share/htslib-test/test/test_expr.c -rw-r--r-- root/root 16603 2026-07-09 09:41 ./usr/share/htslib-test/test/test_faidx.c -rw-r--r-- root/root 13375 2026-07-09 09:41 ./usr/share/htslib-test/test/test_hfile_libcurl.c -rw-r--r-- root/root 2869 2026-07-09 09:41 ./usr/share/htslib-test/test/test_index.c -rw-r--r-- root/root 3313 2026-07-09 09:41 ./usr/share/htslib-test/test/test_introspection.c -rw-r--r-- root/root 3639 2026-07-09 09:41 ./usr/share/htslib-test/test/test_kfunc.c -rw-r--r-- root/root 13601 2026-07-09 09:41 ./usr/share/htslib-test/test/test_khash.c -rw-r--r-- root/root 22976 2026-07-09 09:41 ./usr/share/htslib-test/test/test_kstring.c -rw-r--r-- root/root 7628 2026-07-09 09:41 ./usr/share/htslib-test/test/test_mod.c -rw-r--r-- root/root 4542 2026-07-09 09:41 ./usr/share/htslib-test/test/test_nibbles.c -rw-r--r-- root/root 5057 2026-07-09 09:41 ./usr/share/htslib-test/test/test_realn.c -rw-r--r-- root/root 8892 2026-07-09 09:41 ./usr/share/htslib-test/test/test_str2int.c -rw-r--r-- root/root 4581 2026-07-09 09:41 ./usr/share/htslib-test/test/test_time_funcs.c -rw-r--r-- root/root 15046 2026-07-09 09:41 ./usr/share/htslib-test/test/test_view.c -rw-r--r-- root/root 1688 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads1.c -rw-r--r-- root/root 1621 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads2.c -rw-r--r-- root/root 1729 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads3.c -rw-r--r-- root/root 2310 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads4.c -rw-r--r-- root/root 2176 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads5.c -rw-r--r-- root/root 3452 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads6.c -rw-r--r-- root/root 3693 2026-07-09 09:41 ./usr/share/htslib-test/test/thrash_threads7.c -rw-r--r-- root/root 2938 2026-07-09 09:41 ./usr/share/htslib-test/test/thread_pool.md drwxr-xr-x root/root 0 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/ -rw-r--r-- root/root 2437 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/README -rw-r--r-- root/root 517 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a4.cram -rw-r--r-- root/root 144 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a4.sam -rw-r--r-- root/root 517 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a5.cram -rw-r--r-- root/root 144 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a5.sam -rw-r--r-- root/root 534 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a7.cram -rw-r--r-- root/root 223 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a7.sam -rw-r--r-- root/root 533 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a7b.cram -rw-r--r-- root/root 223 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a7b.sam -rw-r--r-- root/root 534 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a8.cram -rw-r--r-- root/root 223 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a8.sam -rw-r--r-- root/root 533 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a8b.cram -rw-r--r-- root/root 223 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a8b.sam -rw-r--r-- root/root 545 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a9.cram -rw-r--r-- root/root 221 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a9.sam -rw-r--r-- root/root 545 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a9b.cram -rw-r--r-- root/root 221 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/a9b.sam -rw-r--r-- root/root 542 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b7.cram -rw-r--r-- root/root 235 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b7.sam -rw-r--r-- root/root 539 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b7b.cram -rw-r--r-- root/root 235 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b7b.sam -rw-r--r-- root/root 542 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b8.cram -rw-r--r-- root/root 235 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b8.sam -rw-r--r-- root/root 539 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b8b.cram -rw-r--r-- root/root 235 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/b8b.sam -rw-r--r-- root/root 545 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c7.cram -rw-r--r-- root/root 235 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c7.sam -rw-r--r-- root/root 545 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c7b.cram -rw-r--r-- root/root 235 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c7b.sam -rw-r--r-- root/root 534 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c8.cram -rw-r--r-- root/root 223 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c8.sam -rw-r--r-- root/root 533 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c8b.cram -rw-r--r-- root/root 223 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/c8b.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4.cram -rw-r--r-- root/root 189 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4b.cram -rw-r--r-- root/root 189 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4b.sam -rw-r--r-- root/root 519 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4c.cram -rw-r--r-- root/root 188 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4c.sam -rw-r--r-- root/root 519 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4d.cram -rw-r--r-- root/root 188 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4d.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4e.cram -rw-r--r-- root/root 189 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4e.sam -rw-r--r-- root/root 519 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4f.cram -rw-r--r-- root/root 188 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d4f.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5.cram -rw-r--r-- root/root 190 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5b.cram -rw-r--r-- root/root 189 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5b.sam -rw-r--r-- root/root 519 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5c.cram -rw-r--r-- root/root 188 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5c.sam -rw-r--r-- root/root 519 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5d.cram -rw-r--r-- root/root 189 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5d.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5e.cram -rw-r--r-- root/root 189 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5e.sam -rw-r--r-- root/root 516 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5f.cram -rw-r--r-- root/root 190 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d5f.sam -rw-r--r-- root/root 525 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d7.cram -rw-r--r-- root/root 247 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d7.sam -rw-r--r-- root/root 525 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d7b.cram -rw-r--r-- root/root 247 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/d7b.sam -rwxr-xr-x root/root 1309 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/tlen.sh -rw-r--r-- root/root 2696 2026-07-09 09:41 ./usr/share/htslib-test/test/tlen/tlen.tst -rw-r--r-- root/root 2487 2026-07-09 09:41 ./usr/share/htslib-test/test/usepublic.cpp -rw-r--r-- root/root 1549 2026-07-09 09:41 ./usr/share/htslib-test/test/vcf44_1.expected -rw-r--r-- root/root 1511 2026-07-09 09:41 ./usr/share/htslib-test/test/vcf44_1.vcf -rw-r--r-- root/root 427 2026-07-09 09:41 ./usr/share/htslib-test/test/vcf_meta_meta.vcf -rwxr-xr-x root/root 2358 2026-07-09 09:41 ./usr/share/htslib-test/test/with-shlib.sh -rw-r--r-- root/root 1070 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#MD.sam -rw-r--r-- root/root 1159 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#MD2.sam -rw-r--r-- root/root 71 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#blank.sam -rw-r--r-- root/root 905485 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#large_aux.sam -rw-r--r-- root/root 651 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#large_aux2.sam -rw-r--r-- root/root 22668 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#large_aux_java.cram -rw-r--r-- root/root 254 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#minimal.sam -rw-r--r-- root/root 304 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#pair.sam -rw-r--r-- root/root 298 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#repeated.sam -rw-r--r-- root/root 305 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#repeated2.sam -rw-r--r-- root/root 517 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#rg.sam -rw-r--r-- root/root 1028 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#tlen.sam -rw-r--r-- root/root 1096 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#tlen2.sam -rw-r--r-- root/root 267 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#triplet.sam -rw-r--r-- root/root 134 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#u.sam -rw-r--r-- root/root 320 2026-07-09 09:41 ./usr/share/htslib-test/test/xx#unsorted.sam -rw-r--r-- root/root 86 2026-07-09 09:41 ./usr/share/htslib-test/test/xx.fa -rw-r--r-- root/root 44 2026-07-09 09:41 ./usr/share/htslib-test/test/xx.fa.fai -rw-r--r-- root/root 11998 2026-07-09 09:41 ./usr/share/htslib-test/textutils.c -rw-r--r-- root/root 15642 2026-07-09 09:41 ./usr/share/htslib-test/textutils_internal.h -rw-r--r-- root/root 46040 2026-07-09 09:41 ./usr/share/htslib-test/thread_pool.c -rw-r--r-- root/root 5853 2026-07-09 09:41 ./usr/share/htslib-test/thread_pool_internal.h -rw-r--r-- root/root 232828 2026-07-09 09:41 ./usr/share/htslib-test/vcf.c -rw-r--r-- root/root 5570 2026-07-09 09:41 ./usr/share/htslib-test/vcf_sweep.c -rw-r--r-- root/root 57390 2026-07-09 09:41 ./usr/share/htslib-test/vcfutils.c -rwxr-xr-x root/root 2231 2026-09-21 09:43 ./usr/share/htslib-test/version.sh drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 313 2026-09-21 09:43 ./usr/share/lintian/overrides/htslib-test libhts-dev_1.24-2_amd64.deb --------------------------- new Debian package, version 2.0. size 1917060 bytes: control archive=2048 bytes. 1222 bytes, 27 lines control 2485 bytes, 38 lines md5sums Package: libhts-dev Source: htslib Version: 1.24-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8160 Depends: libbz2-dev, libhts3t64 (= 1.24-2), 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 2026-09-21 09:43 ./ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/include/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/include/htslib/ -rw-r--r-- root/root 17985 2026-07-09 09:41 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 24614 2026-07-09 09:41 ./usr/include/htslib/cram.h -rw-r--r-- root/root 15102 2026-07-09 09:41 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 14065 2026-07-09 09:41 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 58286 2026-07-09 09:41 ./usr/include/htslib/hts.h -rw-r--r-- root/root 11143 2026-07-09 09:41 ./usr/include/htslib/hts_alloc.h -rw-r--r-- root/root 4948 2026-07-09 09:41 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 11729 2026-07-09 09:41 ./usr/include/htslib/hts_endian.h -rw-r--r-- root/root 5991 2026-07-09 09:41 ./usr/include/htslib/hts_expr.h -rw-r--r-- root/root 3958 2026-07-09 09:41 ./usr/include/htslib/hts_log.h -rw-r--r-- root/root 2842 2026-07-09 09:41 ./usr/include/htslib/hts_os.h -rw-r--r-- root/root 5646 2026-07-09 09:41 ./usr/include/htslib/kbitset.h -rw-r--r-- root/root 2828 2026-07-09 09:41 ./usr/include/htslib/kfunc.h -rw-r--r-- root/root 28269 2026-07-09 09:41 ./usr/include/htslib/khash.h -rw-r--r-- root/root 4050 2026-07-09 09:41 ./usr/include/htslib/khash_str2int.h -rw-r--r-- root/root 5189 2026-07-09 09:41 ./usr/include/htslib/klist.h -rw-r--r-- root/root 3733 2026-07-09 09:41 ./usr/include/htslib/knetfile.h -rw-r--r-- root/root 3295 2026-07-09 09:41 ./usr/include/htslib/kroundup.h -rw-r--r-- root/root 9357 2026-07-09 09:41 ./usr/include/htslib/kseq.h -rw-r--r-- root/root 11585 2026-07-09 09:41 ./usr/include/htslib/ksort.h -rw-r--r-- root/root 14267 2026-07-09 09:41 ./usr/include/htslib/kstring.h -rw-r--r-- root/root 8881 2026-07-09 09:41 ./usr/include/htslib/regidx.h -rw-r--r-- root/root 93048 2026-07-09 09:41 ./usr/include/htslib/sam.h -rw-r--r-- root/root 20839 2026-07-09 09:41 ./usr/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root 5194 2026-07-09 09:41 ./usr/include/htslib/tbx.h -rw-r--r-- root/root 12969 2026-07-09 09:41 ./usr/include/htslib/thread_pool.h -rw-r--r-- root/root 71003 2026-07-09 09:41 ./usr/include/htslib/vcf.h -rw-r--r-- root/root 1686 2026-07-09 09:41 ./usr/include/htslib/vcf_sweep.h -rw-r--r-- root/root 4919 2026-07-09 09:41 ./usr/include/htslib/vcfutils.h drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 7789186 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.1.24 drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 669 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 2680 2026-07-09 09:41 ./usr/share/doc/libhts-dev/README -rw-r--r-- root/root 2961 2026-07-09 09:41 ./usr/share/doc/libhts-dev/README.large_positions.md.gz -rw-r--r-- root/root 401 2026-09-21 09:43 ./usr/share/doc/libhts-dev/README.test -rw-r--r-- root/root 2560 2026-09-21 09:43 ./usr/share/doc/libhts-dev/changelog.Debian.gz -rw-r--r-- root/root 45327 2026-07-09 09:41 ./usr/share/doc/libhts-dev/changelog.gz -rw-r--r-- root/root 3951 2026-09-21 09:43 ./usr/share/doc/libhts-dev/copyright drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 152 2026-09-21 09:43 ./usr/share/lintian/overrides/libhts-dev libhts3t64-dbgsym_1.24-2_amd64.deb ---------------------------------- new Debian package, version 2.0. size 1555148 bytes: control archive=724 bytes. 517 bytes, 13 lines control 424 bytes, 4 lines md5sums Package: libhts3t64-dbgsym Source: htslib Version: 1.24-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1607 Depends: libhts3t64 (= 1.24-2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libhts3t64 Build-Ids: 0da8051f9c162107d55283c54d6f40b3909b00c8 66f4e9ba448907acd06021bc7f75c19140f1677c 780b923bc2245196770f0c2d755d358db3978ec8 cccef3df476eff8051542255c8bf7b8710ca48a3 drwxr-xr-x root/root 0 2026-09-21 09:43 ./ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/0d/ -rw-r--r-- root/root 53104 2026-09-21 09:43 ./usr/lib/debug/.build-id/0d/a8051f9c162107d55283c54d6f40b3909b00c8.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/66/ -rw-r--r-- root/root 1470864 2026-09-21 09:43 ./usr/lib/debug/.build-id/66/f4e9ba448907acd06021bc7f75c19140f1677c.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/78/ -rw-r--r-- root/root 90088 2026-09-21 09:43 ./usr/lib/debug/.build-id/78/0b923bc2245196770f0c2d755d358db3978ec8.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/cc/ -rw-r--r-- root/root 16992 2026-09-21 09:43 ./usr/lib/debug/.build-id/cc/cef3df476eff8051542255c8bf7b8710ca48a3.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-09-21 09:43 ./usr/share/doc/libhts3t64-dbgsym -> libhts3t64 libhts3t64_1.24-2_amd64.deb --------------------------- new Debian package, version 2.0. size 506296 bytes: control archive=6064 bytes. 1223 bytes, 24 lines control 797 bytes, 11 lines md5sums 30 bytes, 1 lines shlibs 28990 bytes, 898 lines symbols 65 bytes, 2 lines triggers Package: libhts3t64 Source: htslib Version: 1.24-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1173 Depends: libbz2-1.0, libc6 (>= 2.38), libcurl4-gnutls (>= 8.20.0-3~), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), libssl3t64 (>= 3.0.0), zlib1g (>= 1:1.1.4) Breaks: libhts3 (<< 1.24-2), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~) Replaces: libhts3 Provides: libhts3 (= 1.24-2) 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 2026-09-21 09:43 ./ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/htslib/ -rw-r--r-- root/root 14248 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 39016 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 55208 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 981104 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/libhts.so.1.24 lrwxrwxrwx root/root 0 2026-09-21 09:43 ./usr/lib/x86_64-linux-gnu/libhts.so.3 -> libhts.so.1.24 drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/libhts3t64/ -rw-r--r-- root/root 2560 2026-09-21 09:43 ./usr/share/doc/libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 45327 2026-07-09 09:41 ./usr/share/doc/libhts3t64/changelog.gz -rw-r--r-- root/root 3951 2026-09-21 09:43 ./usr/share/doc/libhts3t64/copyright drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/man/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2026-09-21 09:43 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1537 2026-09-21 09:43 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2026-09-21 09:43 ./usr/share/man/man5/vcf.5.gz drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/man/man7/ -rw-r--r-- root/root 3416 2026-09-21 09:43 ./usr/share/man/man7/htslib-s3-plugin.7.gz tabix-dbgsym_1.24-2_amd64.deb ----------------------------- new Debian package, version 2.0. size 3515164 bytes: control archive=656 bytes. 444 bytes, 12 lines control 318 bytes, 3 lines md5sums Package: tabix-dbgsym Source: htslib Version: 1.24-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3977 Depends: tabix (= 1.24-2) Section: debug Priority: optional Description: debug symbols for tabix Build-Ids: 546577d7f0e62f54b97aca609aeb3dfe79721199 63e2bb80173e4b10203cc85ec066ea6baf0340e3 a5766d24f42d5e46854678ddb0974a356c41cc77 drwxr-xr-x root/root 0 2026-09-21 09:43 ./ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/54/ -rw-r--r-- root/root 1138584 2026-09-21 09:43 ./usr/lib/debug/.build-id/54/6577d7f0e62f54b97aca609aeb3dfe79721199.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/63/ -rw-r--r-- root/root 1479800 2026-09-21 09:43 ./usr/lib/debug/.build-id/63/e2bb80173e4b10203cc85ec066ea6baf0340e3.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/lib/debug/.build-id/a5/ -rw-r--r-- root/root 1439968 2026-09-21 09:43 ./usr/lib/debug/.build-id/a5/766d24f42d5e46854678ddb0974a356c41cc77.debug drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-09-21 09:43 ./usr/share/doc/tabix-dbgsym -> tabix tabix_1.24-2_amd64.deb ---------------------- new Debian package, version 2.0. size 533420 bytes: control archive=1136 bytes. 1014 bytes, 21 lines control 545 bytes, 9 lines md5sums Package: tabix Source: htslib Version: 1.24-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2451 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. Commands: bgzip, htsfile, tabix drwxr-xr-x root/root 0 2026-09-21 09:43 ./ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/bin/ -rwxr-xr-x root/root 698664 2026-09-21 09:43 ./usr/bin/bgzip -rwxr-xr-x root/root 854280 2026-09-21 09:43 ./usr/bin/htsfile -rwxr-xr-x root/root 882952 2026-09-21 09:43 ./usr/bin/tabix drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/doc/tabix/ -rw-r--r-- root/root 2561 2026-09-21 09:43 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 45327 2026-07-09 09:41 ./usr/share/doc/tabix/changelog.gz -rw-r--r-- root/root 3951 2026-09-21 09:43 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/man/ drwxr-xr-x root/root 0 2026-09-21 09:43 ./usr/share/man/man1/ -rw-r--r-- root/root 3062 2026-09-21 09:43 ./usr/share/man/man1/bgzip.1.gz -rw-r--r-- root/root 1916 2026-09-21 09:43 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 3647 2026-09-21 09:43 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 22 Sep 2026 07:27:38 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 22 Sep 2026 07:27:38 +0000 | +------------------------------------------------------------------------------+ Purging /build/htslib-P9Y9DS Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 22 Sep 2026 07:27:39 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 105512 Build-Time: 206 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 12 Job: /srv/debomatic/incoming/htslib_1.24-2.dsc Machine Architecture: amd64 Package: htslib Package-Time: 225 Source-Version: 1.24-2 Space: 105512 Status: successful Version: 1.24-2 -------------------------------------------------------------------------------- Finished at 2026-09-22T07:27:35Z Build needed 00:03:45, 105512k disk space