sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | htslib 1.20+ds-2 (amd64) Tue, 21 Jan 2025 04:44:44 +0000 | +==============================================================================+ Package: htslib Version: 1.20+ds-2 Source Version: 1.20+ds-2 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Tue, 21 Jan 2025 04:44:45 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.20+ds-2 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.20+ds-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 21 Jan 2025 04:44:45 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 http://deb.debian.org/debian unstable InRelease [205 kB] Get:3 http://localhost:3142/debian sid InRelease [205 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [68.8 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [68.8 kB] Get:7 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [66.7 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-21-0210.33-F-2025-01-20-0805.29.pdiff [66.7 kB] Fetched 673 kB in 3s (223 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Tue, 21 Jan 2025 04:44:50 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/htslib_1.20+ds-2.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 21 Jan 2025 04:44:50 +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 (>= 1.0), 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 (>= 1.0), build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive ./ InRelease Get:2 copy:/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive ./ Release [609 B] Ign:3 copy:/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive ./ Release.gpg Get:4 copy:/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive ./ Sources [735 B] Get:5 copy:/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive ./ Packages [774 B] Fetched 2118 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... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhtscodecs-dev libhtscodecs2 libicu72 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 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 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 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 gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhtscodecs-dev libhtscodecs2 libicu72 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 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 37.9 MB of archives. After this operation, 131 MB of additional disk space will be used. Get:1 copy:/build/htslib-ZaJraT/resolver-KXAAaM/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 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 1.0.21+nmu1 [248 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1+b1 [475 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-1 [3000 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Preconfiguring packages ... Fetched 37.9 MB in 0s (144 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up libhtscodecs-dev:amd64 (1.6.1-1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libgnutls-dane0t64:amd64 (3.8.8-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libldap-dev:amd64 (2.6.9+dfsg-1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-1) ... Setting up libssl-dev:amd64 (3.4.0-2) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libnghttp3-dev:amd64 (1.6.0-2) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up libdeflate-dev:amd64 (1.23-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libtool (2.5.4-2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libngtcp2-dev:amd64 (1.9.1-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up debhelper (13.24.1) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.1-1+b1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 21 Jan 2025 04:44:58 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Tue, 21 Jan 2025 04:44:58 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.23 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-2 dirmngr_2.2.46-1+b1 dpkg_1.22.14 dpkg-dev_1.22.14 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.3.0-12 g++-13-x86-64-linux-gnu_13.3.0-12 g++-14_14.2.0-14 g++-14-x86-64-linux-gnu_14.2.0-14 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-12 gcc-13-base_13.3.0-12 gcc-13-x86-64-linux-gnu_13.3.0-12 gcc-14_14.2.0-14 gcc-14-base_14.2.0-14 gcc-14-x86-64-linux-gnu_14.2.0-14 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gnupg_2.2.46-1 gnupg-l10n_2.2.46-1 gnupg-utils_2.2.46-1+b1 gpg_2.2.46-1+b1 gpg-agent_2.2.46-1+b1 gpg-wks-client_2.2.46-1+b1 gpgconf_2.2.46-1+b1 gpgsm_2.2.46-1+b1 gpgv_2.2.46-1+b1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-4 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.23 libarchive-zip-perl_1.68-1 libasan8_14.2.0-14 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-14 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbinutils_2.43.50.20250108-1 libblkid1_2.40.4-1 libbrotli-dev_1.1.0-2+b6 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc-l10n_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-14 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libcurl3t64-gnutls_8.11.1-1+b1 libcurl4-gnutls-dev_8.11.1-1+b1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdeflate-dev_1.23-1+b1 libdeflate0_1.23-1+b1 libdpkg-perl_1.22.14 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-12 libgcc-14-dev_14.2.0-14 libgcc-s1_14.2.0-14 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.8-2 libgnutls-openssl27t64_3.8.8-2 libgnutls28-dev_3.8.8-2 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-14 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libgssapi-krb5-2_1.21.3-4 libgssrpc4t64_1.21.3-4 libhogweed6t64_3.10-1+b1 libhtscodecs-dev_1.6.1-1 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-14 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 libidn2-dev_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-14 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-4 libkadm5clnt-mit12_1.21.3-4 libkadm5srv-mit12_1.21.3-4 libkdb5-10t64_1.21.3-4 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-4 libkrb5-dev_1.21.3-4 libkrb5support0_1.21.3-4 libksba8_1.6.7-2+b1 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.9+dfsg-1 libldap2_2.6.9+dfsg-1 liblsan0_14.2.0-14 liblz4-1_1.9.4-4 liblzma-dev_5.6.3-1+b1 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.4-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnghttp2-dev_1.64.0-1 libnghttp3-9_1.6.0-2 libnghttp3-dev_1.6.0-2 libngtcp2-16_1.9.1-1 libngtcp2-crypto-gnutls-dev_1.9.1-1 libngtcp2-crypto-gnutls8_1.9.1-1 libngtcp2-dev_1.9.1-1 libnpth0t64_1.8-2 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpcre2-8-0_10.44-5 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-1 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_14.2.0-14 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8+b1 libsasl2-modules-db_2.1.28+dfsg1-8+b1 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20250108-1 libsmartcols1_2.40.4-1 libsqlite3-0_3.46.1-1 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.4.0-2 libssl3t64_3.4.0-2 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 libsystemd0_257.2-2 libtasn1-6_4.19.0-3+b3 libtasn1-6-dev_4.19.0-3+b3 libtinfo6_6.5-2+b1 libtool_2.5.4-2 libtsan2_14.2.0-14 libubsan1_14.2.0-14 libuchardet0_0.0.8-1+b2 libudev1_257.2-2 libunbound8_1.22.0-1+b1 libunistring5_1.3-1 libuuid1_2.40.4-1 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxxhash0_0.8.3-2 libzstd-dev_1.5.6+dfsg-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.10-1 locales-all_2.40-5 login_1:4.16.0-2+really2.40.4-1 login.defs_1:4.16.0-7 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 nettle-dev_3.10-1+b1 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.1-1 perl-base_5.40.1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-1 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sqv_1.2.1-5 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.40.4-1 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Tue, 21 Jan 2025 04:44:58 +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: 1.20+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.7.0 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 (>= 1.0) 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: d685d071f21fd45109b7a388916dd74d36d3f141 1530935 htslib_1.20+ds.orig.tar.bz2 ed1ec2ef97ea23cb65ce59969398c747499391ba 21272 htslib_1.20+ds-2.debian.tar.xz Checksums-Sha256: 4c7fd2331a58419d310e2de2d649e731bb48e848fcf2ce0c2a4b878731ac024a 1530935 htslib_1.20+ds.orig.tar.bz2 3b04daf8f667979acf0b5fb6c8f5de20d9b8a164a3b22b476a6ecc07d1e0b4cd 21272 htslib_1.20+ds-2.debian.tar.xz Files: 9b37ee27664bdb6b8114e587a190e3a5 1530935 htslib_1.20+ds.orig.tar.bz2 d78bfc2de4b4cf0c7cf2a22892087064 21272 htslib_1.20+ds-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmcjwAoACgkQQc5/C58b izJMbQf/Zqj+Od5csLnq8qJtPNv+brULtfzGB/4HY+npQTtl/ObA0W1nde5wV4nd Odxpv2k8XnH2/YvvRcEx2QPThgFC2/vEy5E3m4hiGn+YZRZUpUsyoE/P1huAQe9p MIxjkf9wqw/HS4ZBf9UdQ2w7+SJvVl/wMP3C3XKjsVc35na+XuU5CTz5EJSXi6xi mbK4bcPQN4I9MzU9yQJVDolsb74zI3dVOUkmfG3Eac+0vOBQZZfySlFaXfVbEEEG ThH/CKMG3GfPbdUR9p5ifagGa23K71Gr+3w6jqpeA00IQyOnfeJ0PhRgWrTw+pRR QeXnLbOL+KQb1/DSxqhkhpnKcpLm3g== =zufe -----END PGP SIGNATURE----- gpgv: Signature made Thu Oct 31 17:36:10 2024 UTC gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./htslib_1.20+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting htslib in /build/htslib-ZaJraT/htslib-1.20+ds dpkg-source: info: unpacking htslib_1.20+ds.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.20+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying cram_to_bam_export.patch dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Tue, 21 Jan 2025 04:44:59 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.20+ds-2 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.20+ds-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 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-ZaJraT/htslib-1.20+ds SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-c514ec1d-cdaf-48d7-8289-432a7d1f4f3d 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 1.20+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from htslib-1.20+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' dh_auto_clean make -j2 distclean make[2]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* test/faidx/FAIL* \ test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/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 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_kstring test/test_mod 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[2]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' rm -rf test_backup/ make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' 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 htslib-1.20+ds/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_1.20+ds.orig.tar.bz2 dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building htslib in htslib_1.20+ds-2.debian.tar.xz dpkg-source: info: building htslib in htslib_1.20+ds-2.dsc debian/rules binary dh binary dh_update_autotools_config cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp mv debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3 cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp mv debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b cp -f /usr/share/misc/config.sub ./config.sub 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 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-ZaJraT/htslib-1.20+ds' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/x86_64-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/x86_64-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking 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 pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... 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 whether fdatasync is declared... yes checking for fdatasync... 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 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-ZaJraT/htslib-1.20+ds' 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-ZaJraT/htslib-1.20+ds' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.20" \ libdir=/usr/lib/x86_64-linux-gnu make -j2 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -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=1.20 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-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 "1.20"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o annot-tsv.o annot-tsv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico 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 gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o 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 synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread 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-ZaJraT/htslib-1.20+ds' make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' 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-ZaJraT/htslib-1.20+ds' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.20" \ 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-ZaJraT/htslib-1.20+ds=. -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=1.20 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' test/hts_endian test/test_expr test/test_kfunc test/test_kstring 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 && REF_PATH=: ./test.pl ${TEST_OPTS:-} 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-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -b -m 14 -x /tmp/pdE9uvpMYD/index.bam.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -b -m 0 -x /tmp/pdE9uvpMYD/index.bam.bai /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -b /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -z -m 14 -x /tmp/pdE9uvpMYD/index.sam.gz.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -z -m 0 -x /tmp/pdE9uvpMYD/index.sam.gz.bai /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -b /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -z -m 14 -x /tmp/pdE9uvpMYD/index.sam.gz.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index_dos.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -z -m 0 -x /tmp/pdE9uvpMYD/index.sam.gz.bai /build/htslib-ZaJraT/htslib-1.20+ds/test/index_dos.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -b /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -C -x /tmp/pdE9uvpMYD/index.cram.crai /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.cram .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index /tmp/pdE9uvpMYD/index.cram .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -b -m 14 -x /tmp/pdE9uvpMYD/index.bcf.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.vcf > /tmp/pdE9uvpMYD/index.bcf .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.bcf .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -z -m 14 -x /tmp/pdE9uvpMYD/index.vcf.gz.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.vcf > /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -l 0 -z -m 0 -x /tmp/pdE9uvpMYD/index.vcf.gz.tbi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.vcf > /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -t /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/tabix /tmp/pdE9uvpMYD/index.vcf.gz##idx##/tmp/pdE9uvpMYD/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 2:2000000-2000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/pdE9uvpMYD/index.bam.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/pdE9uvpMYD/index.bam.bai /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -b /tmp/pdE9uvpMYD/index.bam .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/pdE9uvpMYD/index.sam.gz.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/pdE9uvpMYD/index.sam.gz.bai /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -b /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/pdE9uvpMYD/index.sam.gz.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index_dos.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/pdE9uvpMYD/index.sam.gz.bai /build/htslib-ZaJraT/htslib-1.20+ds/test/index_dos.sam > /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -b /tmp/pdE9uvpMYD/index.sam.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -C -x /tmp/pdE9uvpMYD/index.cram.crai /build/htslib-ZaJraT/htslib-1.20+ds/test/index.sam > /tmp/pdE9uvpMYD/index.cram .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index /tmp/pdE9uvpMYD/index.cram .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/pdE9uvpMYD/index.bcf.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.vcf > /tmp/pdE9uvpMYD/index.bcf .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.bcf .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/pdE9uvpMYD/index.vcf.gz.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.vcf > /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -c /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/pdE9uvpMYD/index.vcf.gz.tbi /build/htslib-ZaJraT/htslib-1.20+ds/test/index.vcf > /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_index -t /tmp/pdE9uvpMYD/index.vcf.gz .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/tabix /tmp/pdE9uvpMYD/index.vcf.gz##idx##/tmp/pdE9uvpMYD/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /tmp/pdE9uvpMYD/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#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 embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [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 .. 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 .. 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-ZaJraT/htslib-1.20+ds/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#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#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 embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [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 .. 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 .. 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-ZaJraT/htslib-1.20+ds/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-ZaJraT/htslib-1.20+ds/test/test-vcf-api /tmp/pdE9uvpMYD/test-vcf-api.bcf .. ok test_bcf2vcf: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /build/htslib-ZaJraT/htslib-1.20+ds/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-vcf-sweep /tmp/pdE9uvpMYD/test-vcf-api.bcf .. ok test_vcf_various: /build/htslib-ZaJraT/htslib-1.20+ds/htsfile -ch /build/htslib-ZaJraT/htslib-1.20+ds/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/htslib-ZaJraT/htslib-1.20+ds/htsfile -c /build/htslib-ZaJraT/htslib-1.20+ds/test/formatcols.vcf .. ok test_vcf_various: /build/htslib-ZaJraT/htslib-1.20+ds/htsfile -c /build/htslib-ZaJraT/htslib-1.20+ds/test/noroundtrip.vcf .. ok test_vcf_various: /build/htslib-ZaJraT/htslib-1.20+ds/htsfile -c /build/htslib-ZaJraT/htslib-1.20+ds/test/formatmissing.vcf .. ok test_vcf_various: /build/htslib-ZaJraT/htslib-1.20+ds/htsfile -c /build/htslib-ZaJraT/htslib-1.20+ds/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view /build/htslib-ZaJraT/htslib-1.20+ds/test/modhdr.vcf.gz chr22:1-2 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 74452500 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 34270147 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 11108528 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 42233895 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 8111117 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 85644070 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 49879942 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 47881429 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 69081244 .. ok test-bcf-sr: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr.pl -t /tmp/pdE9uvpMYD -s 83459376 .. ok test_bcf_sr_no_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.a.vcf /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.b.vcf /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/pdE9uvpMYD/no_index_1.err .. ok test_bcf_sr_no_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.a.vcf /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/pdE9uvpMYD/no_index_2.out 2> /tmp/pdE9uvpMYD/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.a.vcf /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/pdE9uvpMYD/no_index_3.out 2> /tmp/pdE9uvpMYD/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.rec_order.vcf /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/merge.noidx.a.vcf > /tmp/pdE9uvpMYD/no_index_4.out 2> /tmp/pdE9uvpMYD/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -b -p /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf -x /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf.csi /build/htslib-ZaJraT/htslib-1.20+ds/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_1.out.vcf -r '1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_2.out.vcf -r '1:1-2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_4.out.vcf -r '1:1-1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_5.out.vcf -r '{1:1}' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/pdE9uvpMYD/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-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_14.out.vcf -t '1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_15.out.vcf -t '1:1-2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_17.out.vcf -t '1:1-1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_18.out.vcf -t '{1:1}' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/pdE9uvpMYD/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-sr -O vcf -o /tmp/pdE9uvpMYD/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/pdE9uvpMYD/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 test_command: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf-translate - .. ok test_convert_padded_header: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -t ce.fa -C /tmp/pdE9uvpMYD/headernul0.bam .. ok test_convert_padded_header: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -t ce.fa -C /tmp/pdE9uvpMYD/headernul1.bam .. ok test_convert_padded_header: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_view -t ce.fa -C /tmp/pdE9uvpMYD/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/htslib-ZaJraT/htslib-1.20+ds/bgzip -I /build/htslib-ZaJraT/htslib-1.20+ds/test/bgziptest.txt.tmp.gz.gzi -c -g /build/htslib-ZaJraT/htslib-1.20+ds/test/bgziptest.txt .. ok test-logging: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/htslib-ZaJraT/htslib-1.20+ds /build/htslib-ZaJraT/htslib-1.20+ds/test/with-shlib.sh /build/htslib-ZaJraT/htslib-1.20+ds/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn01.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -a -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn01.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -a -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -e -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn01.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -e -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -r -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02-r.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -a -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02_exp.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02.fa -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn02_exp-a.sam -o - .. ok test_realn: /build/htslib-ZaJraT/htslib-1.20+ds/test/test_realn -f /build/htslib-ZaJraT/htslib-1.20+ds/test/realn03.fa -e -i /build/htslib-ZaJraT/htslib-1.20+ds/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/htslib-ZaJraT/htslib-1.20+ds/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap --allow-dups -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl,value:overlap,value -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl,value:overlap,value -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl,value:overlap,value -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -O 0.5 -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -rO 0.5 -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.1.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.2.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.3.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.3.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.3.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl:overlap -a nbp,frac -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.4.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.4.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.4.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.5.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.5.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.5.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.6.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.6.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.6.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.7.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.7.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.7.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.8.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.8.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.8.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.9.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.9.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.9.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -f smpl -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -x -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -x -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -x -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -f smpl -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -f smpl -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -f smpl -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -x -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -x -s /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/src.10.txt | /build/htslib-ZaJraT/htslib-1.20+ds/annot-tsv -m smpl -x -t /build/htslib-ZaJraT/htslib-1.20+ds/test/annot-tsv/dst.10.txt .. ok Number of tests: total .. 293 passed .. 293 failed .. 0 make[2]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' rm -fr -- /tmp/dh-xdg-rundir-RRYD3rh9 make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' 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-ZaJraT/htslib-1.20+ds' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' 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-ZaJraT/htslib-1.20+ds' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/htslib-ZaJraT/htslib-1.20+ds/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.20" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/htslib-ZaJraT/htslib-1.20\+ds/debian/tmp make -j2 install DESTDIR=/build/htslib-ZaJraT/htslib-1.20\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-ZaJraT/htslib-1.20+ds=. -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=1.20 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' mkdir -p -m 755 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/bin /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/include /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/include/htslib /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/share/man/man1 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/share/man/man5 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/share/man/man7 /build/htslib-ZaJraT/htslib-1.20+ds/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-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.20 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.20#g' htslib.pc.tmp > /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.20 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.20 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 chmod 644 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc install -p annot-tsv bgzip htsfile tabix /build/htslib-ZaJraT/htslib-1.20+ds/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-ZaJraT/htslib-1.20+ds/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/htslib-ZaJraT/htslib-1.20+ds/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-ZaJraT/htslib-1.20+ds/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/htslib-ZaJraT/htslib-1.20+ds/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' # 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-ZaJraT/htslib-1.20+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_install-indep make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' dh_install --indep 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 ./config.h ./config.mk ./config_vars.h ./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_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 ./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.h ./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/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/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/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/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_kstring.c ./test/test_mod.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/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\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' dh_install -Nhtslib-test 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.1.20 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/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/htslib-test.debhelper.log debian/rules override_dh_installdocs make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' 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 # 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-ZaJraT/htslib-1.20+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' dh_installchangelogs NEWS install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/.debhelper/generated/libhts3t64/dh_installchangelogs.dch.trimmed debian/libhts3t64/usr/share/doc/libhts3t64/changelog.Debian install -p -m0644 NEWS debian/libhts3t64/usr/share/doc/libhts3t64/changelog install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' 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/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 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 dh_lintian install -m0755 -d debian/libhts3t64/usr/share/lintian/overrides install -p -m0644 debian/libhts3t64.lintian-overrides debian/libhts3t64/usr/share/lintian/overrides/libhts3t64 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.1.20 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.1.20 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 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 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 chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian cd '/build/htslib-ZaJraT/htslib-1.20+ds' cd debian/libhts-dev chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian cd '/build/htslib-ZaJraT/htslib-1.20+ds' cd debian/tabix cd '/build/htslib-ZaJraT/htslib-1.20+ds' chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 cd '/build/htslib-ZaJraT/htslib-1.20+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' dh_fixperms 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 ! -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 debian/libhts3t64/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/usr/share/lintian/overrides -type f -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/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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/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 ! -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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -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 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_missing make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man dh_missing make[1]: Leaving directory '/build/htslib-ZaJraT/htslib-1.20+ds' dh_dwz -a install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.20 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.20: DWARF compression not beneficial - old size 949997 new size 972747 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 rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_strip make[1]: Entering directory '/build/htslib-ZaJraT/htslib-1.20+ds' # 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/4c objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.20 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/4c/1484098c989523bda23f7e165e1d1ea1b6388a.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f/bd27afdb874f1481295e4f75ea1fe985171239.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f/bd27afdb874f1481295e4f75ea1fe985171239.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/9f/bd27afdb874f1481295e4f75ea1fe985171239.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5/ce99e9be8425a8e8a7c58339ec13cc1e0c8b74.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/4c/1484098c989523bda23f7e165e1d1ea1b6388a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.20 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/4c/1484098c989523bda23f7e165e1d1ea1b6388a.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.20 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/d5 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/d5/014fad6c66af92486b91b3bcd829f050d21b71.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/d5/014fad6c66af92486b91b3bcd829f050d21b71.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/d5/014fad6c66af92486b91b3bcd829f050d21b71.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/81 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/81/da536ce0a12cd483280ff660d4b135ee19fa59.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/81/da536ce0a12cd483280ff660d4b135ee19fa59.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/81/da536ce0a12cd483280ff660d4b135ee19fa59.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/dc 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/dc/908c5b7fecc4bae12504dc5fa56e1db0d88846.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/dc/908c5b7fecc4bae12504dc5fa56e1db0d88846.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/dc/908c5b7fecc4bae12504dc5fa56e1db0d88846.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/be 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/be/7bc91099fc4d0fa88a34d079ea762ed3f052f6.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/be/7bc91099fc4d0fa88a34d079ea762ed3f052f6.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/be/7bc91099fc4d0fa88a34d079ea762ed3f052f6.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 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5/ce99e9be8425a8e8a7c58339ec13cc1e0c8b74.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip 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 objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5/ce99e9be8425a8e8a7c58339ec13cc1e0c8b74.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/df objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/df/ee5c26e8b0cdc74c27be0ddfa88c1e568f3b82.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/df/ee5c26e8b0cdc74c27be0ddfa88c1e568f3b82.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/df/ee5c26e8b0cdc74c27be0ddfa88c1e568f3b82.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-ZaJraT/htslib-1.20+ds' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.20+ds)" >> 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.1.20 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.1.20 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=4c1484098c989523bda23f7e165e1d1ea1b6388a 81da536ce0a12cd483280ff660d4b135ee19fa59 be7bc91099fc4d0fa88a34d079ea762ed3f052f6 d5014fad6c66af92486b91b3bcd829f050d21b71 dc908c5b7fecc4bae12504dc5fa56e1db0d88846" -DSection=debug -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=9fbd27afdb874f1481295e4f75ea1fe985171239 d5ce99e9be8425a8e8a7c58339ec13cc1e0c8b74 dfee5c26e8b0cdc74c27be0ddfa88c1e568f3b82" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/tabix chmod 0644 -- debian/libhts-dev/DEBIAN/control chmod 0644 -- debian/tabix/DEBIAN/control dh_md5sums install -m0755 -d debian/libhts3t64/DEBIAN cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/htslib-test/DEBIAN 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 cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums install -m0755 -d debian/libhts-dev/DEBIAN cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums install -m0755 -d debian/tabix/DEBIAN cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.20+ds-2_amd64.deb'. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.20+ds-2_all.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.20+ds-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.20+ds-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'tabix' in '../tabix_1.20+ds-2_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.20+ds-2_amd64.deb'. dpkg-genbuildinfo -O../htslib_1.20+ds-2_amd64.buildinfo dpkg-genchanges -O../htslib_1.20+ds-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from htslib-1.20+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-01-21T04:46:58Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 21 Jan 2025 04:46:58 +0000 | +------------------------------------------------------------------------------+ htslib_1.20+ds-2_amd64.changes: ------------------------------- Format: 1.8 Date: Thu, 31 Oct 2024 18:32:00 +0100 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: source all amd64 Version: 1.20+ds-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Santiago Vila 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 Closes: 1086367 1086368 Changes: htslib (1.20+ds-2) unstable; urgency=medium . * Team upload. * d/control: libhts-dev: Add missing dependency on libbz2-dev. Closes: #1086367, #1086368. Checksums-Sha1: a465ff3e96efe9626ab5a006207892292ecff5a6 1553 htslib_1.20+ds-2.dsc ed1ec2ef97ea23cb65ce59969398c747499391ba 21272 htslib_1.20+ds-2.debian.tar.xz 25a43f5763ec6d1ea2febaa03a140da14e4e8860 1148308 htslib-test_1.20+ds-2_all.deb 9d4dc2cec088bd4dbe32b3ce14a925e0123bd6fe 8479 htslib_1.20+ds-2_amd64.buildinfo 6a8f95b65d2c0f7e54ba3027a1f18fbfe6c31c82 1701564 libhts-dev_1.20+ds-2_amd64.deb 1c966505db4159c6b8dc94e3e0d9a6f481f532c9 1286564 libhts3t64-dbgsym_1.20+ds-2_amd64.deb d892bf78e7ed3d569b895d303eb8c2905b423402 455416 libhts3t64_1.20+ds-2_amd64.deb dd43fcde72cc7d22a5e4809c11fa528b853b7a8c 2972488 tabix-dbgsym_1.20+ds-2_amd64.deb 952b32092fbc9bb7bb0363c54ed4ca1236b281dc 486260 tabix_1.20+ds-2_amd64.deb Checksums-Sha256: 8922054e7ae9fe810a4fc8662052e166782d5315d5bfba1f1f306d0228adab7c 1553 htslib_1.20+ds-2.dsc 3b04daf8f667979acf0b5fb6c8f5de20d9b8a164a3b22b476a6ecc07d1e0b4cd 21272 htslib_1.20+ds-2.debian.tar.xz 18ab4f20d880c262a1882f94ee898bc64596fcb4116d9a0ce835866f8ac60d16 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htslib_1.20+ds-2_amd64.buildinfo a25200790de0b671e20003938e082bab 1701564 libdevel optional libhts-dev_1.20+ds-2_amd64.deb 2f40f67cbdb0ae348063f25fd27cb64e 1286564 debug optional libhts3t64-dbgsym_1.20+ds-2_amd64.deb 7b1d6d74df1c62b199a706510a824a65 455416 libs optional libhts3t64_1.20+ds-2_amd64.deb 06fca0abe54e492f2edbe26595d42cd5 2972488 debug optional tabix-dbgsym_1.20+ds-2_amd64.deb 4220c4972a61daa921ee4c877686b749 486260 science optional tabix_1.20+ds-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 21 Jan 2025 04:46:59 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: all amd64 source Version: 1.20+ds-2 Checksums-Md5: e8351c7e265e6640e0abe2da52f8cf81 1553 htslib_1.20+ds-2.dsc 940209e85906847a5ffdbaf4865596e2 1148308 htslib-test_1.20+ds-2_all.deb 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8922054e7ae9fe810a4fc8662052e166782d5315d5bfba1f1f306d0228adab7c 1553 htslib_1.20+ds-2.dsc 18ab4f20d880c262a1882f94ee898bc64596fcb4116d9a0ce835866f8ac60d16 1148308 htslib-test_1.20+ds-2_all.deb fc245714b5af0e10cbc02830c35fd44220393e21ebddd11929d3c8cac745d1ee 1701564 libhts-dev_1.20+ds-2_amd64.deb 7e91a3625ff15c01dbd226a63560cef7e7994c5ec9a11486487b03be282a4a2c 1286564 libhts3t64-dbgsym_1.20+ds-2_amd64.deb b18f3407499f3a9803d597fd0cb81a0960e60fc7f5cfa99e8ba53a69a1f6a3e6 455416 libhts3t64_1.20+ds-2_amd64.deb 5c530fe4ec9447152a04835bcd10b3dd4ccafe48f63eaa795c44d4f5f64bb328 2972488 tabix-dbgsym_1.20+ds-2_amd64.deb 43d6180a2be37a95fa8722bb3be6a64244e44f6a7901c7fdd78a53e88bfe7dcd 486260 tabix_1.20+ds-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 21 Jan 2025 04:46:58 +0000 Build-Path: /build/htslib-ZaJraT/htslib-1.20+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-1), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-4), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-14), libatomic1 (= 14.2.0-14), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libbinutils (= 2.43.50.20250108-1), libblkid1 (= 2.40.4-1), libbrotli-dev (= 1.1.0-2+b6), libbrotli1 (= 1.1.0-2+b6), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcc1-0 (= 14.2.0-14), libcom-err2 (= 1.47.2-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libcurl3t64-gnutls (= 8.11.1-1+b1), libcurl4-gnutls-dev (= 8.11.1-1+b1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdeflate-dev (= 1.23-1+b1), libdeflate0 (= 1.23-1+b1), libdpkg-perl (= 1.22.14), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.8-2), libgnutls-openssl27t64 (= 3.8.8-2), libgnutls28-dev (= 3.8.8-2), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-14), libgprofng0 (= 2.43.50.20250108-1), libgssapi-krb5-2 (= 1.21.3-4), libgssrpc4t64 (= 1.21.3-4), libhogweed6t64 (= 3.10-1+b1), libhtscodecs-dev (= 1.6.1-1), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-14), libicu72 (= 72.1-6), libidn2-0 (= 2.3.7-2+b1), libidn2-dev (= 2.3.7-2+b1), libisl23 (= 0.27-1), libitm1 (= 14.2.0-14), libjansson4 (= 2.14-2+b3), libk5crypto3 (= 1.21.3-4), libkadm5clnt-mit12 (= 1.21.3-4), libkadm5srv-mit12 (= 1.21.3-4), libkdb5-10t64 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-4), libkrb5-dev (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), libldap-dev (= 2.6.9+dfsg-1), libldap2 (= 2.6.9+dfsg-1), liblsan0 (= 14.2.0-14), liblzma-dev (= 5.6.3-1+b1), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnghttp2-dev (= 1.64.0-1), libnghttp3-9 (= 1.6.0-2), libnghttp3-dev (= 1.6.0-2), libngtcp2-16 (= 1.9.1-1), libngtcp2-crypto-gnutls-dev (= 1.9.1-1), libngtcp2-crypto-gnutls8 (= 1.9.1-1), libngtcp2-dev (= 1.9.1-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpcre2-8-0 (= 10.44-5), libperl5.40 (= 5.40.1-1), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 14.2.0-14), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8+b1), libsasl2-modules-db (= 2.1.28+dfsg1-8+b1), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsframe1 (= 2.43.50.20250108-1), libsmartcols1 (= 2.40.4-1), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.4.0-2), libssl3t64 (= 3.4.0-2), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libsystemd0 (= 257.2-2), libtasn1-6 (= 4.19.0-3+b3), libtasn1-6-dev (= 4.19.0-3+b3), libtinfo6 (= 6.5-2+b1), libtool (= 2.5.4-2), libtsan2 (= 14.2.0-14), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.2-2), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-1), libuuid1 (= 2.40.4-1), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libzstd-dev (= 1.5.6+dfsg-2), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), nettle-dev (= 3.10-1+b1), openssl-provider-legacy (= 3.4.0-2), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), util-linux (= 2.40.4-1), xz-utils (= 5.6.3-1+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1730395920" +------------------------------------------------------------------------------+ | Package contents Tue, 21 Jan 2025 04:46:59 +0000 | +------------------------------------------------------------------------------+ htslib-test_1.20+ds-2_all.deb ----------------------------- new Debian package, version 2.0. size 1148308 bytes: control archive=11320 bytes. 963 bytes, 23 lines control 34974 bytes, 449 lines md5sums Package: htslib-test Source: htslib Version: 1.20+ds-2 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 7979 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 2024-10-31 17:32 ./ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/htslib-test/ -rw-r--r-- root/root 3651 2024-10-31 17:32 ./usr/share/doc/htslib-test/changelog.Debian.gz -rw-r--r-- root/root 36455 2024-04-15 14:09 ./usr/share/doc/htslib-test/changelog.gz -rw-r--r-- root/root 5897 2024-10-31 17:28 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 641 2024-10-31 17:28 ./usr/share/doc/libhts-dev/run-unit-test drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/htslib-test/ -rw-r--r-- root/root 47480 2024-10-31 17:32 ./usr/share/htslib-test/Makefile -rw-r--r-- root/root 34134 2024-01-18 16:09 ./usr/share/htslib-test/annot-tsv.c -rw-r--r-- root/root 22986 2021-08-12 11:13 ./usr/share/htslib-test/bcf_sr_sort.c -rw-r--r-- root/root 3869 2019-09-12 21:26 ./usr/share/htslib-test/bcf_sr_sort.h -rw-r--r-- root/root 83159 2024-04-05 09:17 ./usr/share/htslib-test/bgzf.c -rw-r--r-- root/root 29976 2024-02-13 11:54 ./usr/share/htslib-test/bgzip.c -rw-r--r-- root/root 4914 2024-10-31 17:32 ./usr/share/htslib-test/config.h -rw-r--r-- root/root 4249 2024-10-31 17:32 ./usr/share/htslib-test/config.mk -rw-r--r-- root/root 482 2024-10-31 17:32 ./usr/share/htslib-test/config_vars.h drwxr-xr-x root/root 0 2024-10-31 17:32 ./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 125340 2023-11-16 16:08 ./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 125515 2024-10-31 17:32 ./usr/share/htslib-test/cram/cram_decode.c -rw-r--r-- root/root 4379 2024-10-31 17:32 ./usr/share/htslib-test/cram/cram_decode.h -rw-r--r-- root/root 149257 2024-02-01 16:48 ./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 26994 2023-06-11 17:50 ./usr/share/htslib-test/cram/cram_external.c -rw-r--r-- root/root 23915 2023-11-24 22:49 ./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 176623 2024-04-05 09:17 ./usr/share/htslib-test/cram/cram_io.c -rw-r--r-- root/root 18192 2024-02-06 13:22 ./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 29665 2023-11-20 17:23 ./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 13994 2023-03-29 16:35 ./usr/share/htslib-test/cram/open_trace_file.c -rw-r--r-- root/root 5027 2020-01-07 16:06 ./usr/share/htslib-test/cram/open_trace_file.h -rw-r--r-- root/root 6922 2024-10-31 17:32 ./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 29083 2024-02-08 11:39 ./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 81901 2023-11-16 17:46 ./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 40898 2024-04-05 09:17 ./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 49206 2023-09-23 02:59 ./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 24154 2022-05-30 17:34 ./usr/share/htslib-test/hfile_s3_write.c -rw-r--r-- root/root 167614 2024-02-22 16:33 ./usr/share/htslib-test/hts.c -rw-r--r-- root/root 28360 2022-07-14 09:33 ./usr/share/htslib-test/hts_expr.c -rw-r--r-- root/root 6011 2024-02-22 16:33 ./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 2024-10-31 17:32 ./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 9514 2024-01-18 16:09 ./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 180 2024-10-31 17:32 ./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 -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 2024-04-15 14:09 ./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 -rw-r--r-- root/root 20001 2023-05-30 10:31 ./usr/share/htslib-test/regidx.c -rw-r--r-- root/root 7744 2019-10-02 13:26 ./usr/share/htslib-test/region.c -rw-r--r-- root/root 203581 2024-10-31 17:32 ./usr/share/htslib-test/sam.c -rw-r--r-- root/root 3487 2021-04-16 16:21 ./usr/share/htslib-test/sam_internal.h -rw-r--r-- root/root 25791 2024-04-05 09:17 ./usr/share/htslib-test/sam_mods.c -rw-r--r-- root/root 48669 2023-06-15 09:18 ./usr/share/htslib-test/synced_bcf_reader.c -rw-r--r-- root/root 30342 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./usr/share/lintian/overrides/ -rw-r--r-- root/root 104 2024-10-31 17:28 ./usr/share/lintian/overrides/htslib-test libhts-dev_1.20+ds-2_amd64.deb ------------------------------ new Debian package, version 2.0. size 1701564 bytes: control archive=1984 bytes. 1228 bytes, 27 lines control 2347 bytes, 36 lines md5sums Package: libhts-dev Source: htslib Version: 1.20+ds-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 7063 Depends: libbz2-dev, libhts3t64 (= 1.20+ds-2), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, zlib1g-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. . For compatibility with sambamba, the internal routine cram_to_bam was exported, hereto adopting a patch found in guix. drwxr-xr-x root/root 0 2024-10-31 17:32 ./ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/include/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/include/htslib/ -rw-r--r-- root/root 16469 2023-07-20 15:01 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 22175 2023-01-20 10:05 ./usr/include/htslib/cram.h -rw-r--r-- root/root 15122 2023-07-20 15:01 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 13578 2023-09-08 16:43 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 57362 2024-04-15 14:09 ./usr/include/htslib/hts.h -rw-r--r-- root/root 4445 2024-02-08 14:40 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 11729 2023-08-24 15:40 ./usr/include/htslib/hts_endian.h -rw-r--r-- root/root 5991 2022-07-14 09:33 ./usr/include/htslib/hts_expr.h -rw-r--r-- root/root 3958 2022-05-13 15:25 ./usr/include/htslib/hts_log.h -rw-r--r-- 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debug Priority: optional Multi-Arch: same Description: debug symbols for libhts3t64 Build-Ids: 4c1484098c989523bda23f7e165e1d1ea1b6388a 81da536ce0a12cd483280ff660d4b135ee19fa59 be7bc91099fc4d0fa88a34d079ea762ed3f052f6 d5014fad6c66af92486b91b3bcd829f050d21b71 dc908c5b7fecc4bae12504dc5fa56e1db0d88846 drwxr-xr-x root/root 0 2024-10-31 17:32 ./ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/4c/ -rw-r--r-- root/root 1221472 2024-10-31 17:32 ./usr/lib/debug/.build-id/4c/1484098c989523bda23f7e165e1d1ea1b6388a.debug drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/81/ -rw-r--r-- root/root 14880 2024-10-31 17:32 ./usr/lib/debug/.build-id/81/da536ce0a12cd483280ff660d4b135ee19fa59.debug drwxr-xr-x root/root 0 2024-10-31 17:32 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------------------------------ new Debian package, version 2.0. size 455416 bytes: control archive=6104 bytes. 1296 bytes, 24 lines control 954 bytes, 13 lines md5sums 33 bytes, 1 lines shlibs 30193 bytes, 932 lines symbols 68 bytes, 2 lines triggers Package: libhts3t64 Source: htslib Version: 1.20+ds-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1108 Depends: libbz2-1.0, libc6 (>= 2.34), libcurl3t64-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), libssl3t64 (>= 3.0.0), zlib1g (>= 1:1.1.4) Breaks: ivar (<< 1.3.1~), libhts-dev (<< 1.13~), libhts3 (<< 1.20+ds-2), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~) Replaces: libhts-dev (<< 1.13~), libhts3 Provides: libhts3 (= 1.20+ds-2) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. drwxr-xr-x root/root 0 2024-10-31 17:32 ./ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/htslib/ -rw-r--r-- root/root 14408 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 38984 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 38984 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 22600 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so -rw-r--r-- root/root 907376 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/libhts.so.1.20 lrwxrwxrwx root/root 0 2024-10-31 17:32 ./usr/lib/x86_64-linux-gnu/libhts.so.3 -> libhts.so.1.20 drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/libhts3t64/ -rw-r--r-- root/root 3652 2024-10-31 17:32 ./usr/share/doc/libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 36455 2024-04-15 14:09 ./usr/share/doc/libhts3t64/changelog.gz -rw-r--r-- root/root 5897 2024-10-31 17:28 ./usr/share/doc/libhts3t64/copyright drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 54 2024-10-31 17:28 ./usr/share/lintian/overrides/libhts3t64 drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/man/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2024-10-31 17:32 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1537 2024-10-31 17:32 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2024-10-31 17:32 ./usr/share/man/man5/vcf.5.gz drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/man/man7/ -rw-r--r-- root/root 3416 2024-10-31 17:32 ./usr/share/man/man7/htslib-s3-plugin.7.gz tabix-dbgsym_1.20+ds-2_amd64.deb -------------------------------- new Debian package, version 2.0. size 2972488 bytes: control archive=708 bytes. 450 bytes, 12 lines control 400 bytes, 4 lines md5sums Package: tabix-dbgsym Source: htslib Version: 1.20+ds-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3445 Depends: tabix (= 1.20+ds-2) Section: debug Priority: optional Description: debug symbols for tabix Build-Ids: 9fbd27afdb874f1481295e4f75ea1fe985171239 d5ce99e9be8425a8e8a7c58339ec13cc1e0c8b74 dfee5c26e8b0cdc74c27be0ddfa88c1e568f3b82 drwxr-xr-x root/root 0 2024-10-31 17:32 ./ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/9f/ -rw-r--r-- root/root 1243688 2024-10-31 17:32 ./usr/lib/debug/.build-id/9f/bd27afdb874f1481295e4f75ea1fe985171239.debug drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/d5/ -rw-r--r-- root/root 980880 2024-10-31 17:32 ./usr/lib/debug/.build-id/d5/ce99e9be8425a8e8a7c58339ec13cc1e0c8b74.debug drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.build-id/df/ -rw-r--r-- root/root 1210072 2024-10-31 17:32 ./usr/lib/debug/.build-id/df/ee5c26e8b0cdc74c27be0ddfa88c1e568f3b82.debug drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 77280 2024-10-31 17:32 ./usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-10-31 17:32 ./usr/share/doc/tabix-dbgsym -> tabix tabix_1.20+ds-2_amd64.deb ------------------------- new Debian package, version 2.0. size 486260 bytes: control archive=1128 bytes. 985 bytes, 20 lines control 545 bytes, 9 lines md5sums Package: tabix Source: htslib Version: 1.20+ds-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2293 Depends: libbz2-1.0, libc6 (>= 2.34), 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 2024-10-31 17:32 ./ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/bin/ -rwxr-xr-x root/root 661960 2024-10-31 17:32 ./usr/bin/bgzip -rwxr-xr-x root/root 797096 2024-10-31 17:32 ./usr/bin/htsfile -rwxr-xr-x root/root 821672 2024-10-31 17:32 ./usr/bin/tabix drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/doc/tabix/ -rw-r--r-- root/root 3651 2024-10-31 17:32 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 36455 2024-04-15 14:09 ./usr/share/doc/tabix/changelog.gz -rw-r--r-- root/root 5897 2024-10-31 17:28 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/man/ drwxr-xr-x root/root 0 2024-10-31 17:32 ./usr/share/man/man1/ -rw-r--r-- root/root 3060 2024-10-31 17:32 ./usr/share/man/man1/bgzip.1.gz -rw-r--r-- root/root 1917 2024-10-31 17:32 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 3420 2024-10-31 17:32 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 21 Jan 2025 04:47:00 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 21 Jan 2025 04:47:00 +0000 | +------------------------------------------------------------------------------+ Purging /build/htslib-ZaJraT Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 21 Jan 2025 04:47:00 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 92368 Build-Time: 119 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 8 Job: /srv/debomatic/incoming/htslib_1.20+ds-2.dsc Machine Architecture: amd64 Package: htslib Package-Time: 134 Source-Version: 1.20+ds-2 Space: 92368 Status: successful Version: 1.20+ds-2 -------------------------------------------------------------------------------- Finished at 2025-01-21T04:46:58Z Build needed 00:02:14, 92368k disk space