sbuild (Debian sbuild) 0.91.9 (05 May 2026) on carme.larted.org.uk +==============================================================================+ | htslib 1.22.1+ds2-1 (amd64) Sun, 28 Jun 2026 12:12:26 +0000 | +==============================================================================+ Package: htslib Version: 1.22.1+ds2-1 Source Version: 1.22.1+ds2-1 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 Sun, 28 Jun 2026 12:12:27 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.22.1+ds2-1 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.22.1+ds2-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 28 Jun 2026 12:12:27 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 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 [3039 B] 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 Sun, 28 Jun 2026 12:12:29 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/htslib_1.22.1+ds2-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 28 Jun 2026 12:12:29 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev, build-essential Filtered Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/htslib-pACl65/resolver-EjE4MN/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/htslib-pACl65/resolver-EjE4MN/apt_archive ./ InRelease Get:2 copy:/build/htslib-pACl65/resolver-EjE4MN/apt_archive ./ Release [609 B] Ign:3 copy:/build/htslib-pACl65/resolver-EjE4MN/apt_archive ./ Release.gpg Get:4 copy:/build/htslib-pACl65/resolver-EjE4MN/apt_archive ./ Sources [726 B] Get:5 copy:/build/htslib-pACl65/resolver-EjE4MN/apt_archive ./ Packages [765 B] Fetched 2100 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 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 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 30.3 MB/30.6 MB of archives. After this operation, 116 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.13+dfsg-1+b1 [308 kB] Get:2 copy:/build/htslib-pACl65/resolver-EjE4MN/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [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 1.0-1 [332 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 2.42.2-1 [100.0 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 1:1.18.1-4 [877 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-1 [820 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.2 [77.1 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [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 0.195-1 [58.1 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-1 [2660 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 14.2 [933 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 1.2.0-3 [320 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-1 [416 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.25.1-1+b1 [619 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 0.26.2-3 [222 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 1.69.0-1 [128 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.22.0-1 [29.8 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 3.6.3-1 [3025 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-4 [393 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b2 [372 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.21.0-1 [546 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 1.6.6-1 [101 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.6-1 [3004 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Preconfiguring packages ... Fetched 30.3 MB in 0s (169 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14526 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_1.0-1_amd64.deb ... Unpacking gettext-base (1.0-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... 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Unpacking libhtscodecs-dev:amd64 (1.6.6-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../82-liblzma-dev_5.8.3-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.3-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../83-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.6-1) ... 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-3+b2) ... Setting up bsdextrautils (2.42.2-1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libdebhelper-perl (14.2) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up libpsl5t64:amd64 (0.22.0-1) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up gettext-base (1.0-1) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up libhtscodecs-dev:amd64 (1.6.6-1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.25.1-1+b1) ... 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 (2.6.13+dfsg-1+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libssl-dev:amd64 (3.6.3-1) ... Setting up autopoint (1.0-1) ... 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 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-4) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libp11-kit-dev:amd64 (0.26.2-3) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.22.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-4) ... 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 (8.21.0-1) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... 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 (14.2) ... 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 (8.21.0-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 28 Jun 2026 12:12:35 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sun, 28 Jun 2026 12:12:35 +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_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.0.13-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.2 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-1 gettext-base_1.0-1 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.3.2-3 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1 libcc1-0_16.1.0-2 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl4-gnutls_8.21.0-1 libcurl4-gnutls-dev_8.21.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.2 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhtscodecs-dev_1.6.6-1 libhtscodecs2_1.6.6-1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.0-1 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_1.8.0-3 libldap-dev_2.6.13+dfsg-1+b1 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b2 libp11-kit-dev_0.26.2-3 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-6 libpam-modules-bin_1.7.0-6 libpam-runtime_1.7.0-6 libpam0g_1.7.0-6 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc1-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.22.0-1 libpsl5t64_0.22.0-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssh2-1-dev_1.11.1-4 libssh2-1t64_1.11.1-4 libssl-dev_3.6.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunbound8_1.25.1-1+b1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-3+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.13-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc1-1 perl-base_5.44.0~rc1-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc1-1 pinentry-curses_1.3.2-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.3.0-5+b2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 28 Jun 2026 12:12:35 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htslib Binary: libhts3t64, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.22.1+ds2-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3t64 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: ce3c0511527a8bc8a3327cf6aaa38b28ec271e0c 1593472 htslib_1.22.1+ds2.orig.tar.bz2 47a81c0b05b2700d0660b453fa5ddb3ded7e5cb4 22004 htslib_1.22.1+ds2-1.debian.tar.xz Checksums-Sha256: 911a26eb37943726c5f616bd8044144dbdcc0c127e8770f6b82ed0627f3dbd80 1593472 htslib_1.22.1+ds2.orig.tar.bz2 e97c8951ce5ff4d80c7dc3f2c0b8a4b73ddf18f7d219f2b15aaf104af4b28018 22004 htslib_1.22.1+ds2-1.debian.tar.xz Files: 435ce1c1b723732c43d0925889e2d3d4 1593472 htslib_1.22.1+ds2.orig.tar.bz2 ded83a10f428ad5a72615e496d651719 22004 htslib_1.22.1+ds2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmi5imkSHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+biGAYP/1aC/QvynNdNcVe3ikuDnnZFhSiQbj4k 3m39CS5oS5ZjJuNW2GaZvEZHcPWoUjb7bwjbkh9oee9D2fK8JezxAe5ILnB0PA6K BMfn9mzDcrLiJSSUk++wUzog79XIT2YW63l1wSc0MAtaJyNUJZomDjcvOCoQX/j0 7Rz77h6TkkO60isA7e30AKToL+u0SeNzD8MkiJDJbE0NxhxGgd/zhM8w+RlK3VnM MbpjepUwV2GxD0IIEt6hPgF6cbZWR4guBQPClrvb7ZYpn5uIf19vE9xMyDw6mRB8 Bz892I2NyYsotOtsa+i7qy/SNKMtXdYB2pCglpJPOcqsx6DFUqsC4QeO2K14YiDA roBlRukKPfrOFyc+uXvXInyW4BiROux7fV7EBhz8msfrN9MQX7K8rJzLt7hB+gCt +CqZEepEOldbdMCRGpD/YBD01BvtdP87MJeqkeoqVbpz5+yuG3TYtalYQmTut6ky FmFXCUjsb5TySqRMB09sOUyqd+raWjjLyU/J/PeA5Jy1VrctWvGkeTiYCQjhroG2 f+lZxtxqBholSfwMXGTwc4ayDDUM3Rj3eudCEjeB2l6qVsOESLTZfGwtZKNEbg5g vEXGVqxpUozr3FvisF3Lk7HS81k1r9juqr6Ss5S3cjh8WFrX1wskJIcu0y8MicwV tCS6yVoks8/2 =DUBu -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./htslib_1.22.1+ds2-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./htslib_1.22.1+ds2-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting htslib in /build/htslib-pACl65/htslib-1.22.1+ds2 dpkg-source: info: unpacking htslib_1.22.1+ds2.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.22.1+ds2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sun, 28 Jun 2026 12:12:36 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.22.1+ds2-1 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.22.1+ds2-1 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-pACl65/htslib-1.22.1+ds2 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-af3cefdd-2274-4c28-a2f0-21da01cacec5 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.22.1+ds2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from /build/htslib-pACl65/htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean dh_auto_clean make -j2 distclean make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \ test/longrefs/*.tmp.* test/ref_cache/*.tmp.* test/tabix/*.tmp.* \ test/bgzf_boundaries/*.tmp.* test/*/FAIL* \ header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f ref_cache/*.o rm -f libhts.a annot-tsv bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_faidx test/test_kfunc test/test_khash test/test_kstring test/test_mod test/test_nibbles test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' rm -rf test_backup/ make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3t64/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) dpkg-source -Zxz -b . dpkg-source: info: using options from /build/htslib-pACl65/htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building htslib using existing ../htslib_1.22.1+ds2.orig.tar.bz2 dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building htslib in ../htslib_1.22.1+ds2-1.debian.tar.xz dpkg-source: info: building htslib in ../htslib_1.22.1+ds2-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i -v autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: 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-pACl65/htslib-1.22.1+ds2' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/x86_64-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/x86_64-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib checking for gcc... 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 C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt checking C compiler flags needed for avx2... -mavx2 -mpopcnt checking C compiler flags needed for avx512f... -mavx512f -mpopcnt checking for working __builtin_cpu_supports("ssse3")... yes checking for working __attribute__((target("ssse3")))... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for 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 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-pACl65/htslib-1.22.1+ds2' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu make -j2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" CPPFLAGS="-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.22.1"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ '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-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o simd.o simd.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration 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test/test_nibbles.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/http_parser.o ref_cache/http_parser.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time 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-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-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/ref_files.o ref_cache/ref_files.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/request_handler.o ref_cache/request_handler.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/server.o ref_cache/server.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/transaction.o ref_cache/transaction.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/upstream.o ref_cache/upstream.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c 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_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 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 -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_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread 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 -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 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_kstring test/test_kstring.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 make[2]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j2 test TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" CPPFLAGS="-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && \ if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ else \ REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ fi bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 14 -x /tmp/r6MUtTuHAI/index.bam.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 0 -x /tmp/r6MUtTuHAI/index.bam.bai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -b /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/r6MUtTuHAI/index.sam.gz.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/r6MUtTuHAI/index.sam.gz.bai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -b /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/r6MUtTuHAI/index.sam.gz.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/r6MUtTuHAI/index.sam.gz.bai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -b /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -C -x /tmp/r6MUtTuHAI/index.cram.crai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.cram .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index /tmp/r6MUtTuHAI/index.cram .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 14 -x /tmp/r6MUtTuHAI/index.bcf.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.vcf > /tmp/r6MUtTuHAI/index.bcf .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.bcf .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/r6MUtTuHAI/index.vcf.gz.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.vcf > /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/r6MUtTuHAI/index.vcf.gz.tbi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.vcf > /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -t /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/tabix /tmp/r6MUtTuHAI/index.vcf.gz##idx##/tmp/r6MUtTuHAI/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 2:2000000-2000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 14 -x /tmp/r6MUtTuHAI/index.bam.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 0 -x /tmp/r6MUtTuHAI/index.bam.bai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -b /tmp/r6MUtTuHAI/index.bam .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/r6MUtTuHAI/index.sam.gz.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/r6MUtTuHAI/index.sam.gz.bai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -b /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/r6MUtTuHAI/index.sam.gz.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/r6MUtTuHAI/index.sam.gz.bai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -b /tmp/r6MUtTuHAI/index.sam.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -C -x /tmp/r6MUtTuHAI/index.cram.crai /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.sam > /tmp/r6MUtTuHAI/index.cram .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index /tmp/r6MUtTuHAI/index.cram .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 14 -x /tmp/r6MUtTuHAI/index.bcf.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.vcf > /tmp/r6MUtTuHAI/index.bcf .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.bcf .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/r6MUtTuHAI/index.vcf.gz.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.vcf > /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/r6MUtTuHAI/index.vcf.gz.tbi /build/htslib-pACl65/htslib-1.22.1+ds2/test/index.vcf > /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -t /tmp/r6MUtTuHAI/index.vcf.gz .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/tabix /tmp/r6MUtTuHAI/index.vcf.gz##idx##/tmp/r6MUtTuHAI/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /tmp/r6MUtTuHAI/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#bounds_er.tmp.cram.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-vcf-api /tmp/r6MUtTuHAI/test-vcf-api.bcf .. ok test_bcf2vcf: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /build/htslib-pACl65/htslib-1.22.1+ds2/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-vcf-sweep /tmp/r6MUtTuHAI/test-vcf-api.bcf .. ok test_vcf_various: /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile -ch /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile -c /build/htslib-pACl65/htslib-1.22.1+ds2/test/formatcols.vcf .. ok test_vcf_various: /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile -c /build/htslib-pACl65/htslib-1.22.1+ds2/test/noroundtrip.vcf .. ok test_vcf_various: /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile -c /build/htslib-pACl65/htslib-1.22.1+ds2/test/formatmissing.vcf .. ok test_vcf_various: /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile -c /build/htslib-pACl65/htslib-1.22.1+ds2/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view /build/htslib-pACl65/htslib-1.22.1+ds2/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile -c /build/htslib-pACl65/htslib-1.22.1+ds2/test/vcf44_1.vcf .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 74452500 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 34270147 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 11108528 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 42233895 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 8111117 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 85644070 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 49879942 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 47881429 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 69081244 .. ok test-bcf-sr: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/r6MUtTuHAI -s 83459376 .. ok test_bcf_sr_no_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.b.vcf /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/r6MUtTuHAI/no_index_1.err .. ok test_bcf_sr_no_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/r6MUtTuHAI/no_index_2.out 2> /tmp/r6MUtTuHAI/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/r6MUtTuHAI/no_index_3.out 2> /tmp/r6MUtTuHAI/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.rec_order.vcf /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf > /tmp/r6MUtTuHAI/no_index_4.out 2> /tmp/r6MUtTuHAI/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -b -p /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf -x /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf.csi /build/htslib-pACl65/htslib-1.22.1+ds2/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_1.out.vcf -r '1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_2.out.vcf -r '1:1-2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_4.out.vcf -r '1:1-1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_5.out.vcf -r '{1:1}' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/r6MUtTuHAI/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-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_14.out.vcf -t '1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_15.out.vcf -t '1:1-2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_17.out.vcf -t '1:1-1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_18.out.vcf -t '{1:1}' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/r6MUtTuHAI/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/r6MUtTuHAI/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/r6MUtTuHAI/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-pACl65/htslib-1.22.1+ds2/test/test-bcf-translate - .. ok test_convert_padded_header: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/r6MUtTuHAI/headernul0.bam .. ok test_convert_padded_header: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/r6MUtTuHAI/headernul1.bam .. ok test_convert_padded_header: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/r6MUtTuHAI/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/htslib-pACl65/htslib-1.22.1+ds2/bgzip -I /build/htslib-pACl65/htslib-1.22.1+ds2/test/bgziptest.txt.tmp.gz.gzi -c -g /build/htslib-pACl65/htslib-1.22.1+ds2/test/bgziptest.txt .. ok test-logging: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/htslib-pACl65/htslib-1.22.1+ds2 /build/htslib-pACl65/htslib-1.22.1+ds2/test/with-shlib.sh /build/htslib-pACl65/htslib-1.22.1+ds2/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn01.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -a -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn01.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -a -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -e -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn01.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -e -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -r -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02-r.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -a -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02_exp.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02.fa -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn02_exp-a.sam -o - .. ok test_realn: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test_realn -f /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn03.fa -e -i /build/htslib-pACl65/htslib-1.22.1+ds2/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/htslib-pACl65/htslib-1.22.1+ds2/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -f smpl -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -x -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -x -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -x -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -x -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -x -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -m smpl -x -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -s /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt | /build/htslib-pACl65/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -t /build/htslib-pACl65/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok ref-cache: ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam .. ok Number of tests: total .. 352 passed .. 352 failed .. 0 make[2]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' rm -fr -- /tmp/dh-xdg-rundir-39PUdRB1 make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3t64/ debian/libhts3t64/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/htslib-test/ debian/htslib-test/ debian/.debhelper/generated/tabix/ debian/tabix/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/htslib-pACl65/htslib-1.22.1+ds2/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/htslib-pACl65/htslib-1.22.1\+ds2/debian/tmp make -j2 install DESTDIR=/build/htslib-pACl65/htslib-1.22.1\+ds2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-pACl65/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" CPPFLAGS="-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' mkdir -p -m 755 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/bin /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/include /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/include/htslib /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man5 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man7 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig if test -n "/usr/lib/x86_64-linux-gnu/htslib"; then mkdir -p -m 755 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.22.1#g' htslib.pc.tmp > /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.22.1 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so chmod 644 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.22.1 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ install -p -m 644 ref_cache/ref-cache.1 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 ; \ fi install -p -m 644 faidx.5 sam.5 vcf.5 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/htslib-pACl65/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_install install -m0755 -d debian/libhts3t64/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/htslib debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 debian/libhts3t64/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts3t64/usr/share/man/man5 cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man5/ install -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -m0755 -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -m0755 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./annot-tsv.c ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./builddir_vars.mk.in ./config.h.in ./config.mk.in ./configure.ac ./errmod.c ./faidx.c ./fuzz_settings.h ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_expr.c ./hts_internal.h ./hts_os.c ./hts_time_funcs.h ./htscodecs.mk ./htscodecs_bundled.mk ./htscodecs_external.mk ./htsfile.c ./htslib.mk ./htslib.pc.in ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./sam_mods.c ./simd.c ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.sh debian/htslib-test/usr/share/htslib-test/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/m4 cp --reflink=auto -a ./m4/hts_check_compile_flags_needed.m4 ./m4/hts_hide_dynamic_syms.m4 ./m4/hts_prog_cc_warnings.m4 ./m4/pkg.m4 debian/htslib-test/usr/share/htslib-test/m4/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/ref_cache cp --reflink=auto -a ./ref_cache/cmsg_wrap.c ./ref_cache/cmsg_wrap.h ./ref_cache/http_parser.c ./ref_cache/http_parser.h ./ref_cache/listener.c ./ref_cache/listener.h ./ref_cache/log_files.c ./ref_cache/log_files.h ./ref_cache/main.c ./ref_cache/misc.c ./ref_cache/misc.h ./ref_cache/options.h ./ref_cache/ping.c ./ref_cache/ping.h ./ref_cache/poll_wrap.h ./ref_cache/poll_wrap_epoll.c ./ref_cache/poll_wrap_poll.c ./ref_cache/ref_files.c ./ref_cache/ref_files.h ./ref_cache/request_handler.c ./ref_cache/request_handler.h ./ref_cache/sendfile_wrap.c ./ref_cache/sendfile_wrap.h ./ref_cache/server.c ./ref_cache/server.h ./ref_cache/transaction.c ./ref_cache/transaction.h ./ref_cache/types.h ./ref_cache/upstream.c ./ref_cache/upstream.h debian/htslib-test/usr/share/htslib-test/ref_cache/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/annot-tsv ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/base_mods ./test/bcf-sr ./test/bgzf_boundaries ./test/bgziptest.txt ./test/bgziptest.txt.gz ./test/bgziptest.txt.gz.gzi ./test/c1\#bounds.sam ./test/c1\#clip.sam ./test/c1\#noseq.sam ./test/c1\#pad1.sam ./test/c1\#pad2.sam ./test/c1\#pad3.sam ./test/c1\#unknown.sam ./test/c1.fa ./test/c1.fa.fai ./test/c2\#pad.sam ./test/c2.fa ./test/c2.fa.fai ./test/ce\#1.sam ./test/ce\#1000.sam ./test/ce\#2.sam ./test/ce\#5.sam ./test/ce\#5b.sam ./test/ce\#5b_java.cram ./test/ce\#large_seq.sam ./test/ce\#supp.sam ./test/ce\#tag_depadded.sam ./test/ce\#tag_padded.sam ./test/ce\#unmap.sam ./test/ce\#unmap1.sam ./test/ce\#unmap2.sam ./test/ce.fa ./test/ce.fa.fai ./test/colons.bam ./test/colons.bam.bai ./test/compare_sam.pl ./test/cross_validate.sh ./test/emptyfile ./test/faidx ./test/fastq ./test/fastqs_README.txt ./test/fieldarith.c ./test/fieldarith.sam ./test/formatcols.vcf ./test/formatmissing-out.vcf ./test/formatmissing.vcf ./test/fuzz ./test/header_syms.pl ./test/hfile.c ./test/hts_endian.c ./test/index.bam.bai ./test/index.bam.csi ./test/index.bcf.csi ./test/index.cram.crai ./test/index.sam ./test/index.sam.gz.bai ./test/index.sam.gz.csi ./test/index.vcf ./test/index.vcf.gz.csi ./test/index.vcf.gz.tbi ./test/index2.sam ./test/index_dos.sam ./test/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/modhdr.expected.vcf ./test/modhdr.vcf.gz ./test/modhdr.vcf.gz.csi ./test/mpileup ./test/no_hdr_sq_1.bam ./test/no_hdr_sq_1.bam.csi ./test/no_hdr_sq_1.expected.sam ./test/noroundtrip-out.vcf ./test/noroundtrip.vcf ./test/pileup.c ./test/pileup_mod.c ./test/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./test/range.out2 ./test/realn01.fa ./test/realn01.fa.fai ./test/realn01.sam ./test/realn01_exp-a.sam ./test/realn01_exp-e.sam ./test/realn01_exp.sam ./test/realn02-r.sam ./test/realn02.fa ./test/realn02.fa.fai ./test/realn02.sam ./test/realn02_exp-a.sam ./test/realn02_exp-e.sam ./test/realn02_exp.sam ./test/realn03.fa ./test/realn03.fa.fai ./test/realn03.sam ./test/realn03_exp.sam ./test/ref_cache ./test/sam.c ./test/sam_filter ./test/simple_test_driver.sh ./test/tabix ./test/tabix.out ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-bcf_set_variant_type.c ./test/test-logging.pl ./test/test-parse-reg.c ./test/test-regidx.c ./test/test-vcf-api.c ./test/test-vcf-api.out ./test/test-vcf-hdr-in.vcf ./test/test-vcf-hdr.out ./test/test-vcf-sweep.c ./test/test-vcf-sweep.out ./test/test.pl ./test/test_bgzf.c ./test/test_expr.c ./test/test_faidx.c ./test/test_index.c ./test/test_introspection.c ./test/test_kfunc.c ./test/test_khash.c ./test/test_kstring.c ./test/test_mod.c ./test/test_nibbles.c ./test/test_realn.c ./test/test_str2int.c ./test/test_time_funcs.c ./test/test_view.c ./test/thrash_threads1.c ./test/thrash_threads2.c ./test/thrash_threads3.c ./test/thrash_threads4.c ./test/thrash_threads5.c ./test/thrash_threads6.c ./test/thrash_threads7.c ./test/thread_pool.md ./test/usepublic.cpp ./test/vcf44_1.expected ./test/vcf44_1.vcf ./test/vcf_meta_meta.vcf ./test/with-shlib.sh ./test/xx\#MD.sam ./test/xx\#MD2.sam ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#u.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules execute_after_dh_install-indep make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_installdocs install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/copyright debian/libhts3t64/usr/share/doc/libhts3t64/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so: No such file or directory make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_installchangelogs NEWS 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 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 make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_installman install -m0755 -d debian/libhts3t64/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/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.1.22.1 debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -s libhts.so.1.22.1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/htslib-test/usr/share/htslib-test/htscodecs.mk ln -s htscodecs_external.mk debian/htslib-test/usr/share/htslib-test/htscodecs.mk install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism Using 1756986990 as canonical time Normalizing debian/htslib-test/usr/share/htslib-test/test/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/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 chmod a-x 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 gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian cd '/build/htslib-pACl65/htslib-1.22.1+ds2' cd '/build/htslib-pACl65/htslib-1.22.1+ds2' cd debian/libhts-dev cd debian/tabix 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 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/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 cd '/build/htslib-pACl65/htslib-1.22.1+ds2' cd '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_fixperms find debian/libhts3t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/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/libhts-dev/usr/include debian/libhts-dev/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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-pACl65/htslib-1.22.1+ds2' find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' debian/rules execute_before_dh_missing make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_missing dh_dwz -a install -m0755 -d debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 dwz: debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1: DWARF compression not beneficial - old size 977805 new size 1001372 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug debian/rules override_dh_strip make[1]: Entering directory '/build/htslib-pACl65/htslib-1.22.1+ds2' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01/789854d4bab2fedb47cf5773470dbddcd2e915.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b0 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b0/5de5cc7a3b9aba1632facc68e4e06aad61188d.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b0/5de5cc7a3b9aba1632facc68e4e06aad61188d.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/01/789854d4bab2fedb47cf5773470dbddcd2e915.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b0/5de5cc7a3b9aba1632facc68e4e06aad61188d.debug debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01/789854d4bab2fedb47cf5773470dbddcd2e915.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe/48e85894e936eccedc46ee9f5482a8391a21bd.debug 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/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/66/ebe4cce108b6da6f9a817264d9884a9e1a40aa.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/66/ebe4cce108b6da6f9a817264d9884a9e1a40aa.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/66/ebe4cce108b6da6f9a817264d9884a9e1a40aa.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/b2 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/b2/567688060fdf1f110360918326ba668feafd26.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/b2/567688060fdf1f110360918326ba668feafd26.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/b2/567688060fdf1f110360918326ba668feafd26.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/0d objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/0d/89feaaa62d4d0846a5af970acfb30c012efe78.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/0d/89feaaa62d4d0846a5af970acfb30c012efe78.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/0d/89feaaa62d4d0846a5af970acfb30c012efe78.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/22 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/22/b4fa753df0f383689522080acdb2dc5c55b5cc.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/22/b4fa753df0f383689522080acdb2dc5c55b5cc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/22/b4fa753df0f383689522080acdb2dc5c55b5cc.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3t64/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc ln -s libhts3t64 debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc/libhts3t64-dbgsym install -m0755 -d debian/.debhelper/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fe/48e85894e936eccedc46ee9f5482a8391a21bd.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/fe/48e85894e936eccedc46ee9f5482a8391a21bd.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/33 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/33/d56d9f4c07fcf69a2d46f7b82ba0e01a186da3.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/33/d56d9f4c07fcf69a2d46f7b82ba0e01a186da3.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/33/d56d9f4c07fcf69a2d46f7b82ba0e01a186da3.debug debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/build/htslib-pACl65/htslib-1.22.1+ds2' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.22.1+ds2)" >> debian/libhts3t64/DEBIAN/shlibs chmod 0644 -- debian/libhts3t64/DEBIAN/shlibs dpkg-gensymbols -plibhts3t64 -Idebian/libhts3t64.symbols -Pdebian/libhts3t64 -edebian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers mv debian/libhts3t64.substvars.new debian/libhts3t64.substvars rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars 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 debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so dh_installdeb install -m0755 -d debian/libhts3t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3t64/triggers debian/libhts3t64/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol install -m0755 -d debian/libhts3t64/DEBIAN echo misc:Depends= >> debian/libhts3t64.substvars echo misc:Pre-Depends= >> debian/libhts3t64.substvars install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/.debhelper/libhts3t64/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libhts3t64-dbgsym -DDepends="libhts3t64 (= \${binary:Version})" -DDescription="debug symbols for libhts3t64" -DBuild-Ids="01789854d4bab2fedb47cf5773470dbddcd2e915 0d89feaaa62d4d0846a5af970acfb30c012efe78 22b4fa753df0f383689522080acdb2dc5c55b5cc 66ebe4cce108b6da6f9a817264d9884a9e1a40aa b2567688060fdf1f110360918326ba668feafd26" -DSection=debug -DMulti-Arch=same -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN echo misc:Depends= >> debian/htslib-test.substvars echo misc:Pre-Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -cdebian/control -Pdebian/htslib-test chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/libhts3t64 chmod 0644 -- debian/htslib-test/DEBIAN/control install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=tabix-dbgsym -DDepends="tabix (= \${binary:Version})" -DDescription="debug symbols for tabix" -DBuild-Ids="33d56d9f4c07fcf69a2d46f7b82ba0e01a186da3 b05de5cc7a3b9aba1632facc68e4e06aad61188d fe48e85894e936eccedc46ee9f5482a8391a21bd" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/tabix chmod 0644 -- debian/libhts3t64/DEBIAN/control install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -cdebian/control -Pdebian/libhts-dev chmod 0644 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts-dev/DEBIAN/control dh_md5sums install -m0755 -d debian/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/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/.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/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/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 'libhts3t64' in '../libhts3t64_1.22.1+ds2-1_amd64.deb'. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.22.1+ds2-1_all.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'tabix' in '../tabix_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.22.1+ds2-1_amd64.deb'. dpkg-genbuildinfo -O../htslib_1.22.1+ds2-1_amd64.buildinfo dpkg-genchanges -O../htslib_1.22.1+ds2-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from /build/htslib-pACl65/htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2026-06-28T12:15:00Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 28 Jun 2026 12:15:01 +0000 | +------------------------------------------------------------------------------+ htslib_1.22.1+ds2-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Thu, 04 Sep 2025 13:56:30 +0200 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: source all amd64 Version: 1.22.1+ds2-1 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: htslib-test - Test data for HTSlib libhts-dev - development files for the HTSlib libhts3t64 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.22.1+ds2-1) unstable; urgency=medium . * Properly clean the upstream release tarball. * Don't ship architecture-specific files in htslib-test; regenerate them at test-time using autoconf. * d/libhts3t64.symbols: add new symbols for the latest release. Checksums-Sha1: f6c6fb11ecdb96e7e941fe91c7c9bf9db3f05c98 1565 htslib_1.22.1+ds2-1.dsc ce3c0511527a8bc8a3327cf6aaa38b28ec271e0c 1593472 htslib_1.22.1+ds2.orig.tar.bz2 6bc3b84150356b5d0f8cb8881401906ef4984238 22000 htslib_1.22.1+ds2-1.debian.tar.xz 181ecff346053624f8d315683f128bf1381f3feb 1223980 htslib-test_1.22.1+ds2-1_all.deb 854bcb41031d75d03fa10f65f37136e5fe5e7ca2 8301 htslib_1.22.1+ds2-1_amd64.buildinfo 0162c20d415bb232e474d5c643bec133b1572ea9 1783640 libhts-dev_1.22.1+ds2-1_amd64.deb 58c753ac8255bbd935fe4ea7ba50f9279c733d1b 1350644 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb cecc8c131eb0ecb4e2d3de5dd26b483bee907aaa 474472 libhts3t64_1.22.1+ds2-1_amd64.deb ae74f7f224b2429a0a0b310ea56056020ec08e06 3126132 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 3406a8bfc2de997f85bcacb25bf21127b7a2094e 507600 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha256: 8a807efc88a64c375869d3efe66db661e2c4b6ccf9f444eecf5d9d222791d396 1565 htslib_1.22.1+ds2-1.dsc 911a26eb37943726c5f616bd8044144dbdcc0c127e8770f6b82ed0627f3dbd80 1593472 htslib_1.22.1+ds2.orig.tar.bz2 12144122391e1e9d992a6c5f3f5017c432c02210555ceb84ff00f09fafec6052 22000 htslib_1.22.1+ds2-1.debian.tar.xz cb7960f05df9ed0ec6009f2244aca7de2bc80eec5fc1f0e42bd6d2fe91b929d2 1223980 htslib-test_1.22.1+ds2-1_all.deb 8573a8507dd52d6ec345fa78bd654549b9023dab79a6825ed0bfa797de9b0d8f 8301 htslib_1.22.1+ds2-1_amd64.buildinfo 74d625a6d33e857a629e144bf4ac5978820e70b4ac8de7025bde8255d85f5a15 1783640 libhts-dev_1.22.1+ds2-1_amd64.deb 6c4ea32b480e4d5cea680b841bbbcabd63d059139ab3d667935180099afd93a5 1350644 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb d3e51694fe2dfd5bd5247c0aea8f2dc445691fe98c337add12eac66c73f3d9bd 474472 libhts3t64_1.22.1+ds2-1_amd64.deb d05ddbbefa0c125d62e6c2ff7ab4adef83e59e9304a7c5906612e51fa3d0f498 3126132 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 4b8f39fccef37d5fc8c805677441f7f855d3ccd676014ee467fcbbdf05c33f39 507600 tabix_1.22.1+ds2-1_amd64.deb Files: 36fd984b46f288559a8d5f1624583e36 1565 science optional htslib_1.22.1+ds2-1.dsc 435ce1c1b723732c43d0925889e2d3d4 1593472 science optional htslib_1.22.1+ds2.orig.tar.bz2 54d5a893e02c66adc774283e54699cd1 22000 science optional htslib_1.22.1+ds2-1.debian.tar.xz e2eab0dc3d36114a12e8bc1a6171486a 1223980 science optional htslib-test_1.22.1+ds2-1_all.deb f0efd4d1db70f8cfba45804e62763ba8 8301 science optional htslib_1.22.1+ds2-1_amd64.buildinfo eccee8f70c032917a8af508d7ae027ba 1783640 libdevel optional libhts-dev_1.22.1+ds2-1_amd64.deb 7939ed11ec5f2c30e10d99a0b9c5e584 1350644 debug optional libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 6852cb69a5dc4fddab81d45b7a7dfde8 474472 libs optional libhts3t64_1.22.1+ds2-1_amd64.deb 159bf7fe72d6b417d2db14a3a62543c6 3126132 debug optional tabix-dbgsym_1.22.1+ds2-1_amd64.deb e3b7f93a7be51f53d6a6adb837e143d1 507600 science optional tabix_1.22.1+ds2-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 28 Jun 2026 12:15:01 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: all amd64 source Version: 1.22.1+ds2-1 Checksums-Md5: 36fd984b46f288559a8d5f1624583e36 1565 htslib_1.22.1+ds2-1.dsc e2eab0dc3d36114a12e8bc1a6171486a 1223980 htslib-test_1.22.1+ds2-1_all.deb eccee8f70c032917a8af508d7ae027ba 1783640 libhts-dev_1.22.1+ds2-1_amd64.deb 7939ed11ec5f2c30e10d99a0b9c5e584 1350644 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 6852cb69a5dc4fddab81d45b7a7dfde8 474472 libhts3t64_1.22.1+ds2-1_amd64.deb 159bf7fe72d6b417d2db14a3a62543c6 3126132 tabix-dbgsym_1.22.1+ds2-1_amd64.deb e3b7f93a7be51f53d6a6adb837e143d1 507600 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha1: f6c6fb11ecdb96e7e941fe91c7c9bf9db3f05c98 1565 htslib_1.22.1+ds2-1.dsc 181ecff346053624f8d315683f128bf1381f3feb 1223980 htslib-test_1.22.1+ds2-1_all.deb 0162c20d415bb232e474d5c643bec133b1572ea9 1783640 libhts-dev_1.22.1+ds2-1_amd64.deb 58c753ac8255bbd935fe4ea7ba50f9279c733d1b 1350644 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb cecc8c131eb0ecb4e2d3de5dd26b483bee907aaa 474472 libhts3t64_1.22.1+ds2-1_amd64.deb ae74f7f224b2429a0a0b310ea56056020ec08e06 3126132 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 3406a8bfc2de997f85bcacb25bf21127b7a2094e 507600 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha256: 8a807efc88a64c375869d3efe66db661e2c4b6ccf9f444eecf5d9d222791d396 1565 htslib_1.22.1+ds2-1.dsc cb7960f05df9ed0ec6009f2244aca7de2bc80eec5fc1f0e42bd6d2fe91b929d2 1223980 htslib-test_1.22.1+ds2-1_all.deb 74d625a6d33e857a629e144bf4ac5978820e70b4ac8de7025bde8255d85f5a15 1783640 libhts-dev_1.22.1+ds2-1_amd64.deb 6c4ea32b480e4d5cea680b841bbbcabd63d059139ab3d667935180099afd93a5 1350644 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb d3e51694fe2dfd5bd5247c0aea8f2dc445691fe98c337add12eac66c73f3d9bd 474472 libhts3t64_1.22.1+ds2-1_amd64.deb d05ddbbefa0c125d62e6c2ff7ab4adef83e59e9304a7c5906612e51fa3d0f498 3126132 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 4b8f39fccef37d5fc8c805677441f7f855d3ccd676014ee467fcbbdf05c33f39 507600 tabix_1.22.1+ds2-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 28 Jun 2026 12:15:00 +0000 Build-Path: /build/htslib-pACl65/htslib-1.22.1+ds2 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-1), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.2), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-1), gettext-base (= 1.0-1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbrotli-dev (= 1.2.0-3), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1), libcc1-0 (= 16.1.0-2), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl4-gnutls (= 8.21.0-1), libcurl4-gnutls-dev (= 8.21.0-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.2), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), 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 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhtscodecs-dev (= 1.6.6-1), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16.1.0-2), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.0-1), 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 (= 2.6.13+dfsg-1+b1), libldap2 (= 2.6.13+dfsg-1+b1), liblsan0 (= 16.1.0-2), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp2-dev (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libnghttp3-dev (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls-dev (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libngtcp2-dev (= 1.22.1-1), libp11-kit-dev (= 0.26.2-3), libp11-kit0 (= 0.26.2-3), libpam-modules (= 1.7.0-6), libpam-modules-bin (= 1.7.0-6), libpam-runtime (= 1.7.0-6), libpam0g (= 1.7.0-6), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc1-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.22.0-1), libpsl5t64 (= 0.22.0-1), libquadmath0 (= 16.1.0-2), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssh2-1-dev (= 1.11.1-4), libssh2-1t64 (= 1.11.1-4), libssl-dev (= 3.6.3-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20251231-1+b1), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunbound8 (= 1.25.1-1+b1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd-dev (= 1.5.7+dfsg-3+b2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.0.13-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1+b1), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc1-1), perl-base (= 5.44.0~rc1-1), perl-modules-5.44 (= 5.44.0~rc1-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1756986990" +------------------------------------------------------------------------------+ | Package contents Sun, 28 Jun 2026 12:15:01 +0000 | +------------------------------------------------------------------------------+ htslib-test_1.22.1+ds2-1_all.deb -------------------------------- new Debian package, version 2.0. size 1223980 bytes: control archive=12784 bytes. 966 bytes, 23 lines control 40017 bytes, 512 lines md5sums Package: htslib-test Source: htslib Version: 1.22.1+ds2-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 8447 Depends: perl:any Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/samtools/htslib Description: Test data for HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains test files and scripts for the HTSlib. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/htslib-test/ -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/htslib-test/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/htslib-test/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 1463 2025-09-04 10:59 ./usr/share/doc/libhts-dev/run-unit-test drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/ -rw-r--r-- root/root 53693 2025-09-04 11:56 ./usr/share/htslib-test/Makefile -rw-r--r-- root/root 40886 2025-05-01 08:41 ./usr/share/htslib-test/annot-tsv.c -rw-r--r-- root/root 23600 2024-10-21 11:11 ./usr/share/htslib-test/bcf_sr_sort.c -rw-r--r-- root/root 4239 2024-10-21 11:11 ./usr/share/htslib-test/bcf_sr_sort.h -rw-r--r-- root/root 83378 2025-04-10 09:08 ./usr/share/htslib-test/bgzf.c -rw-r--r-- root/root 29931 2025-05-01 08:41 ./usr/share/htslib-test/bgzip.c -rw-r--r-- root/root 2487 2021-04-14 18:34 ./usr/share/htslib-test/builddir_vars.mk.in -rw-r--r-- root/root 6316 2025-09-04 11:56 ./usr/share/htslib-test/config.h.in -rw-r--r-- root/root 3973 2025-04-17 09:02 ./usr/share/htslib-test/config.mk.in -rw-r--r-- root/root 33346 2025-06-26 10:58 ./usr/share/htslib-test/configure.ac drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/cram/ -rw-r--r-- root/root 2420 2020-05-20 23:18 ./usr/share/htslib-test/cram/cram.h -rw-r--r-- root/root 125724 2025-07-01 08:45 ./usr/share/htslib-test/cram/cram_codecs.c -rw-r--r-- root/root 8556 2023-01-20 10:05 ./usr/share/htslib-test/cram/cram_codecs.h -rw-r--r-- root/root 126140 2025-07-02 16:31 ./usr/share/htslib-test/cram/cram_decode.c -rw-r--r-- root/root 4572 2024-03-07 15:14 ./usr/share/htslib-test/cram/cram_decode.h -rw-r--r-- root/root 149978 2024-12-09 09:39 ./usr/share/htslib-test/cram/cram_encode.c -rw-r--r-- root/root 3701 2022-07-19 17:16 ./usr/share/htslib-test/cram/cram_encode.h -rw-r--r-- root/root 33270 2024-09-05 15:21 ./usr/share/htslib-test/cram/cram_external.c -rw-r--r-- root/root 29478 2025-01-23 16:57 ./usr/share/htslib-test/cram/cram_index.c -rw-r--r-- root/root 3866 2020-09-16 09:17 ./usr/share/htslib-test/cram/cram_index.h -rw-r--r-- root/root 177280 2025-07-02 12:04 ./usr/share/htslib-test/cram/cram_io.c -rw-r--r-- root/root 18393 2025-07-02 16:31 ./usr/share/htslib-test/cram/cram_io.h -rw-r--r-- root/root 2911 2021-02-03 10:22 ./usr/share/htslib-test/cram/cram_samtools.h -rw-r--r-- root/root 7055 2023-11-09 17:01 ./usr/share/htslib-test/cram/cram_stats.c -rw-r--r-- root/root 2273 2019-11-19 11:20 ./usr/share/htslib-test/cram/cram_stats.h -rw-r--r-- root/root 29792 2024-10-07 10:47 ./usr/share/htslib-test/cram/cram_structs.h -rw-r--r-- root/root 17233 2020-09-16 09:17 ./usr/share/htslib-test/cram/mFILE.c -rw-r--r-- root/root 3075 2019-11-19 11:20 ./usr/share/htslib-test/cram/mFILE.h -rw-r--r-- root/root 3371 2019-11-19 11:20 ./usr/share/htslib-test/cram/misc.h -rw-r--r-- root/root 14867 2025-05-15 09:10 ./usr/share/htslib-test/cram/open_trace_file.c -rw-r--r-- root/root 5150 2025-05-15 09:10 ./usr/share/htslib-test/cram/open_trace_file.h -rw-r--r-- root/root 6922 2025-09-04 11:56 ./usr/share/htslib-test/cram/os.h -rw-r--r-- root/root 5049 2020-01-07 16:06 ./usr/share/htslib-test/cram/pooled_alloc.c -rw-r--r-- root/root 2185 2019-11-19 11:20 ./usr/share/htslib-test/cram/pooled_alloc.h -rw-r--r-- root/root 4422 2020-09-16 09:17 ./usr/share/htslib-test/cram/string_alloc.c -rw-r--r-- root/root 2356 2019-11-19 11:20 ./usr/share/htslib-test/cram/string_alloc.h -rw-r--r-- root/root 6757 2019-11-19 11:20 ./usr/share/htslib-test/errmod.c -rw-r--r-- root/root 30982 2024-08-15 14:18 ./usr/share/htslib-test/faidx.c -rw-r--r-- root/root 1442 2023-08-07 08:39 ./usr/share/htslib-test/fuzz_settings.h -rw-r--r-- root/root 82309 2025-03-06 09:42 ./usr/share/htslib-test/header.c -rw-r--r-- root/root 10466 2020-01-08 16:24 ./usr/share/htslib-test/header.h -rw-r--r-- root/root 41258 2024-11-14 12:29 ./usr/share/htslib-test/hfile.c -rw-r--r-- root/root 5139 2021-06-22 10:24 ./usr/share/htslib-test/hfile_gcs.c -rw-r--r-- root/root 8112 2022-05-13 15:25 ./usr/share/htslib-test/hfile_internal.h -rw-r--r-- root/root 49245 2025-06-02 09:17 ./usr/share/htslib-test/hfile_libcurl.c -rw-r--r-- root/root 41232 2024-04-05 09:17 ./usr/share/htslib-test/hfile_s3.c -rw-r--r-- root/root 24158 2024-04-29 14:17 ./usr/share/htslib-test/hfile_s3_write.c -rw-r--r-- root/root 169188 2025-02-16 23:20 ./usr/share/htslib-test/hts.c -rw-r--r-- root/root 28501 2024-08-15 14:18 ./usr/share/htslib-test/hts_expr.c -rw-r--r-- root/root 5862 2025-04-10 09:08 ./usr/share/htslib-test/hts_internal.h -rw-r--r-- root/root 1981 2021-02-03 10:22 ./usr/share/htslib-test/hts_os.c -rw-r--r-- root/root 5886 2022-07-19 11:03 ./usr/share/htslib-test/hts_time_funcs.h lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/htscodecs.mk -> htscodecs_external.mk -rw-r--r-- root/root 3675 2023-03-15 11:45 ./usr/share/htslib-test/htscodecs_bundled.mk -rw-r--r-- root/root 1710 2021-02-25 16:36 ./usr/share/htslib-test/htscodecs_external.mk -rw-r--r-- root/root 9547 2025-05-01 08:41 ./usr/share/htslib-test/htsfile.c -rw-r--r-- root/root 6976 2023-05-18 14:41 ./usr/share/htslib-test/htslib.mk -rw-r--r-- root/root 484 2024-10-17 18:24 ./usr/share/htslib-test/htslib.pc.in -rw-r--r-- root/root 180 2025-09-04 11:56 ./usr/share/htslib-test/htslib_static.mk -rw-r--r-- root/root 3333 2022-08-16 10:42 ./usr/share/htslib-test/htslib_vars.mk -rw-r--r-- root/root 10879 2021-02-03 10:22 ./usr/share/htslib-test/kfunc.c -rw-r--r-- root/root 11837 2024-04-05 09:17 ./usr/share/htslib-test/kstring.c drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/m4/ -rw-r--r-- root/root 2656 2023-11-08 17:07 ./usr/share/htslib-test/m4/hts_check_compile_flags_needed.m4 -rw-r--r-- root/root 4627 2025-04-17 09:02 ./usr/share/htslib-test/m4/hts_hide_dynamic_syms.m4 -rw-r--r-- root/root 8273 2019-04-18 12:14 ./usr/share/htslib-test/m4/hts_prog_cc_warnings.m4 -rw-r--r-- root/root 10244 2020-06-27 01:17 ./usr/share/htslib-test/m4/pkg.m4 -rw-r--r-- root/root 10656 2019-10-02 13:26 ./usr/share/htslib-test/md5.c -rw-r--r-- root/root 8488 2019-11-19 11:20 ./usr/share/htslib-test/multipart.c drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/htslib-test/os/ -rw-r--r-- root/root 2345 2017-04-26 20:08 ./usr/share/htslib-test/os/lzma_stub.h -rw-r--r-- root/root 2704 2019-10-01 22:06 ./usr/share/htslib-test/os/rand.c -rw-r--r-- root/root 6513 2023-03-29 16:35 ./usr/share/htslib-test/plugin.c -rw-r--r-- root/root 17284 2023-07-20 15:01 ./usr/share/htslib-test/probaln.c -rw-r--r-- root/root 13218 2023-05-23 14:36 ./usr/share/htslib-test/realn.c drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/htslib-test/ref_cache/ -rw-r--r-- root/root 2706 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/cmsg_wrap.c -rw-r--r-- root/root 1384 2025-05-27 22:33 ./usr/share/htslib-test/ref_cache/cmsg_wrap.h -rw-r--r-- root/root 21352 2025-05-23 16:45 ./usr/share/htslib-test/ref_cache/http_parser.c -rw-r--r-- root/root 3616 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/http_parser.h -rw-r--r-- root/root 7560 2025-05-23 16:37 ./usr/share/htslib-test/ref_cache/listener.c -rw-r--r-- root/root 1506 2025-05-09 15:35 ./usr/share/htslib-test/ref_cache/listener.h -rw-r--r-- root/root 9826 2025-05-27 22:43 ./usr/share/htslib-test/ref_cache/log_files.c -rw-r--r-- root/root 1723 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/log_files.h -rw-r--r-- root/root 35233 2025-06-11 09:28 ./usr/share/htslib-test/ref_cache/main.c -rw-r--r-- root/root 2331 2025-05-22 18:43 ./usr/share/htslib-test/ref_cache/misc.c -rw-r--r-- root/root 3263 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/misc.h -rw-r--r-- root/root 2940 2025-05-23 15:49 ./usr/share/htslib-test/ref_cache/options.h -rw-r--r-- root/root 4032 2025-05-23 16:37 ./usr/share/htslib-test/ref_cache/ping.c -rw-r--r-- root/root 1281 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/ping.h -rw-r--r-- root/root 2875 2025-05-26 20:37 ./usr/share/htslib-test/ref_cache/poll_wrap.h -rw-r--r-- root/root 3992 2025-05-26 21:33 ./usr/share/htslib-test/ref_cache/poll_wrap_epoll.c -rw-r--r-- root/root 7439 2025-05-26 21:30 ./usr/share/htslib-test/ref_cache/poll_wrap_poll.c -rw-r--r-- root/root 6061 2025-05-22 18:43 ./usr/share/htslib-test/ref_cache/ref_files.c -rw-r--r-- root/root 2361 2025-04-17 09:02 ./usr/share/htslib-test/ref_cache/ref_files.h -rw-r--r-- root/root 5655 2025-05-26 20:22 ./usr/share/htslib-test/ref_cache/request_handler.c -rw-r--r-- root/root 1595 2025-04-17 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2025-09-04 11:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 313 2024-11-14 19:27 ./usr/share/lintian/overrides/htslib-test libhts-dev_1.22.1+ds2-1_amd64.deb --------------------------------- new Debian package, version 2.0. size 1783640 bytes: control archive=2024 bytes. 1234 bytes, 27 lines control 2420 bytes, 37 lines md5sums Package: libhts-dev Source: htslib Version: 1.22.1+ds2-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 7562 Depends: libbz2-dev, libhts3t64 (= 1.22.1+ds2-1), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, zlib1g-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. . 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Package: libhts3t64-dbgsym Source: htslib Version: 1.22.1+ds2-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1420 Depends: libhts3t64 (= 1.22.1+ds2-1) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libhts3t64 Build-Ids: 01789854d4bab2fedb47cf5773470dbddcd2e915 0d89feaaa62d4d0846a5af970acfb30c012efe78 22b4fa753df0f383689522080acdb2dc5c55b5cc 66ebe4cce108b6da6f9a817264d9884a9e1a40aa b2567688060fdf1f110360918326ba668feafd26 drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/01/ -rw-r--r-- root/root 1288488 2025-09-04 11:56 ./usr/lib/debug/.build-id/01/789854d4bab2fedb47cf5773470dbddcd2e915.debug drwxr-xr-x root/root 0 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2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts3t64-dbgsym -> libhts3t64 libhts3t64_1.22.1+ds2-1_amd64.deb --------------------------------- new Debian package, version 2.0. size 474472 bytes: control archive=6176 bytes. 1241 bytes, 24 lines control 883 bytes, 12 lines md5sums 36 bytes, 1 lines shlibs 30767 bytes, 949 lines symbols 65 bytes, 2 lines triggers Package: libhts3t64 Source: htslib Version: 1.22.1+ds2-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1142 Depends: libbz2-1.0, libc6 (>= 2.38), 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 (<< 1.22.1+ds2-1), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~) Replaces: libhts3 Provides: libhts3 (= 1.22.1+ds2-1) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/ -rw-r--r-- root/root 14408 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 34888 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 43080 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 22600 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so -rw-r--r-- root/root 940144 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/lib/x86_64-linux-gnu/libhts.so.3 -> libhts.so.1.22.1 drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/libhts3t64/ -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/libhts3t64/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/libhts3t64/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2025-09-04 11:56 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1537 2025-09-04 11:56 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2025-09-04 11:56 ./usr/share/man/man5/vcf.5.gz drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/man7/ -rw-r--r-- root/root 3418 2025-09-04 11:56 ./usr/share/man/man7/htslib-s3-plugin.7.gz tabix-dbgsym_1.22.1+ds2-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 3126132 bytes: control archive=704 bytes. 456 bytes, 12 lines control 400 bytes, 4 lines md5sums Package: tabix-dbgsym Source: htslib Version: 1.22.1+ds2-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3603 Depends: tabix (= 1.22.1+ds2-1) Section: debug Priority: optional Description: debug symbols for tabix Build-Ids: 33d56d9f4c07fcf69a2d46f7b82ba0e01a186da3 b05de5cc7a3b9aba1632facc68e4e06aad61188d fe48e85894e936eccedc46ee9f5482a8391a21bd drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/33/ -rw-r--r-- root/root 1273280 2025-09-04 11:56 ./usr/lib/debug/.build-id/33/d56d9f4c07fcf69a2d46f7b82ba0e01a186da3.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/b0/ -rw-r--r-- root/root 1308824 2025-09-04 11:56 ./usr/lib/debug/.build-id/b0/5de5cc7a3b9aba1632facc68e4e06aad61188d.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.build-id/fe/ -rw-r--r-- root/root 1011008 2025-09-04 11:56 ./usr/lib/debug/.build-id/fe/48e85894e936eccedc46ee9f5482a8391a21bd.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 79728 2025-09-04 11:56 ./usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-04 11:56 ./usr/share/doc/tabix-dbgsym -> tabix tabix_1.22.1+ds2-1_amd64.deb ---------------------------- new Debian package, version 2.0. size 507600 bytes: control archive=1128 bytes. 988 bytes, 20 lines control 545 bytes, 9 lines md5sums Package: tabix Source: htslib Version: 1.22.1+ds2-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2365 Depends: libbz2-1.0, libc6 (>= 2.38), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. . This package is built from the HTSlib source, and provides the bgzip, htsfile, and tabix tools. drwxr-xr-x root/root 0 2025-09-04 11:56 ./ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/bin/ -rwxr-xr-x root/root 678344 2025-09-04 11:56 ./usr/bin/bgzip -rwxr-xr-x root/root 825768 2025-09-04 11:56 ./usr/bin/htsfile -rwxr-xr-x root/root 846248 2025-09-04 11:56 ./usr/bin/tabix drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/doc/tabix/ -rw-r--r-- root/root 2281 2025-09-04 11:56 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 41299 2025-07-14 11:11 ./usr/share/doc/tabix/changelog.gz -rw-r--r-- root/root 5925 2025-09-03 10:14 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-04 11:56 ./usr/share/man/man1/ -rw-r--r-- root/root 3064 2025-09-04 11:56 ./usr/share/man/man1/bgzip.1.gz -rw-r--r-- root/root 1919 2025-09-04 11:56 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 3422 2025-09-04 11:56 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 28 Jun 2026 12:15:03 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 28 Jun 2026 12:15:03 +0000 | +------------------------------------------------------------------------------+ Purging /build/htslib-pACl65 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 28 Jun 2026 12:15:04 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 100384 Build-Time: 144 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/htslib_1.22.1+ds2-1.dsc Machine Architecture: amd64 Package: htslib Package-Time: 154 Source-Version: 1.22.1+ds2-1 Space: 100384 Status: successful Version: 1.22.1+ds2-1 -------------------------------------------------------------------------------- Finished at 2026-06-28T12:15:00Z Build needed 00:02:34, 100384k disk space