htslib →
1.9-8 →
armhf → 2019-01-05 05:02:59
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| htslib 1.9-8 (armhf) Sat, 05 Jan 2019 04:54:18 +0000 |
+==============================================================================+
Package: htslib
Version: 1.9-8
Source Version: 1.9-8
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-92b61d6e-302c-4ff3-a387-a3eb956542cf' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.5 MB in 9s (2791 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'htslib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/htslib.git
Please use:
git clone https://salsa.debian.org/med-team/htslib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1302 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main htslib 1.9-8 (dsc) [2325 B]
Get:2 http://172.17.0.1/private buster-staging/main htslib 1.9-8 (tar) [1286 kB]
Get:3 http://172.17.0.1/private buster-staging/main htslib 1.9-8 (diff) [14.2 kB]
Fetched 1302 kB in 0s (6035 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-OGbOSI/htslib-1.9' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-OGbOSI' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-u1U8ng/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-u1U8ng/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-u1U8ng/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15815 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-u1U8ng/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-htslib-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Sources [531 B]
Get:5 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ Packages [611 B]
Fetched 2475 B in 0s (12.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install htslib build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libtool
libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config liblzma-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 libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-htslib-dummy
zlib1g-dev
0 upgraded, 43 newly installed, 0 to remove and 2 not upgraded.
Need to get 20.6 MB/20.9 MB of archives.
After this operation, 74.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-u1U8ng/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-1 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.62.0-1 [284 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.62.0-1 [358 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23+b8 [25.3 kB]
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Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Processing triggers for libc-bin (2.28-2) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.0.0-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.62.0-1) ...
Setting up groff-base (1.22.4-1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcurl4-gnutls-dev:armhf (7.62.0-1) ...
Setting up libtool (2.4.6-6) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Setting up debhelper (12) ...
Setting up dh-exec (0.23+b8) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23+b8 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.1-3 groff-base_1.22.4-1 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1+b1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-13+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.62.0-1 libcurl4-gnutls-dev_7.62.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-13+rpi1 libgcc1_1:8.2.0-13+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-13+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.2-1 libhogweed4_3.4.1~rc1-1 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnss-systemd_240-2+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_240-2+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 libsystemd0_240-2+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-13+rpi1 libuchardet0_0.0.6-3 libudev1_240-2+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-2 tar_1.30+dfsg-3+rpi1 tzdata_2018i-1 udev_240-2+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Dec 31 15:08:34 2018 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./htslib_1.9-8.dsc
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.9.orig.tar.gz
dpkg-source: info: unpacking htslib_1.9-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying fPIC.patch
dpkg-source: info: applying testShebang.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-92b61d6e-302c-4ff3-a387-a3eb956542cf
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.9-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL*
rm -f libhts.so libhts.so.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/sam test/test_bgzf test/test_realn test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/test-bcf-translate test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk
rm -rf autom4te.cache
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf test_backup/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/libhts-private-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
rm -fr -- debian/libhts2/ debian/tmp/ debian/libhts-dev/ debian/libhts-private-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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
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 '/<<PKGBUILDDIR>>'
# create clean copy of test dir
cp -a test test_backup
autoconf
dh_auto_configure -- --enable-libcurl
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... 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 libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
# re-try later LDLIBS=-lhts \
PACKAGE_VERSION="1.9-8" \
libdir=/usr/lib/arm-linux-gnueabihf
make -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_gcs.o hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3.o hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/files.pico cram/files.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.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_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -lcurl -lcrypto
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 test VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
test/hts_endian
test/fieldarith test/fieldarith.sam
test/hfile
test/test_bgzf test/bgziptest.txt
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
Expected passes: 13
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq
test/test-regidx
cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-}
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -S -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 -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=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -t auxf.fa -S -l0 -C -o VERSION=3.0 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 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.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 -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 -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=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -S -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 -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=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -S -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 -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=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -S -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 -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=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -S -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 -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=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -S -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 -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=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view 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 -S -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 -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=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -S -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 -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=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -t c2.fa -S -l0 -C -o VERSION=3.0 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 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.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 -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.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 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view 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#2.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view 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 -S -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 -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=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.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 -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 -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=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > 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 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > 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 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view 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 -S -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 -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=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view 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 -S -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 -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=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view 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_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view 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_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -S -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 -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=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -S -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 -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=2.1 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -t md.fa -S -l0 -C -o VERSION=3.0 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 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram
./test_view -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
./test_view md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view 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 -S -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 -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=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > 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 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > 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 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view 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 -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 -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 -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=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view 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_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view 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 -S -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 -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=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view 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 -S -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 -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=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -S -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 -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=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -@4 -S -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 -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=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view -@4 auxf#values.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view -@4 auxf#values.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view -@4 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view -@4 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 -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 -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=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view -@4 c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -@4 -S -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 -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=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view -@4 c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -@4 -S -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 -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=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view -@4 c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -@4 -S -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 -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=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view -@4 c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -@4 -S -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 -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=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view -@4 c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -@4 -S -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 -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=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view -@4 c1#pad3.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view -@4 c1#pad3.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view -@4 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 -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 -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=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view -@4 c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -@4 -S -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 -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=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -@4 -t c2.fa -S -l0 -C -o VERSION=3.0 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 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view -@4 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view -@4 c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view -@4 ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.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 -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view -@4 ce#1000.tmp.bam.cram.bam > 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 -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 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam
./test_view -@4 ce#1000.tmp.bam.cram.bam > 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=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
./test_view -@4 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#2.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view -@4 ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view -@4 ce#5.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view -@4 ce#5.tmp.bam.cram.bam > 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=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view -@4 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 -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 -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=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view -@4 ce#5b.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view -@4 ce#5b.tmp.bam.cram.bam > 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=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view -@4 ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.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 -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 -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=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view -@4 ce#large_seq.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view -@4 ce#large_seq.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view -@4 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 -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 -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=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view -@4 ce#supp.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view -@4 ce#supp.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view -@4 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 -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 -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=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view -@4 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_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view -@4 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_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view -@4 ce#unmap.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view -@4 ce#unmap.tmp.bam.cram.bam > 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=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view -@4 ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view -@4 ce#unmap1.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view -@4 ce#unmap1.tmp.bam.cram.bam > 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=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view -@4 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -@4 -S -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 -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=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view -@4 ce#unmap2.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view -@4 ce#unmap2.tmp.bam.cram.bam > 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=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view -@4 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok
test_view testing md#1.sam, ref md.fa:
./test_view -@4 -S -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 -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=2.1 md#1.tmp.bam > md#1.tmp.bam.cram
./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t md.fa -S -l0 -C -o VERSION=3.0 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 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam
./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_
./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_
./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram
./test_view -@4 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
./test_view -@4 md#1.tmp.cram > md#1.tmp.cram.sam_
./compare_sam.pl md#1.sam md#1.tmp.cram.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view -@4 xx#blank.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view -@4 xx#blank.tmp.bam.cram.bam > 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=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view -@4 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 -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 -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=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view -@4 xx#large_aux.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view -@4 xx#large_aux.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view -@4 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 -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 -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=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view -@4 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_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view -@4 xx#minimal.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view -@4 xx#minimal.tmp.bam.cram.bam > 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=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view -@4 xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view -@4 xx#pair.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view -@4 xx#pair.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view -@4 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 -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 -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=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view -@4 xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view -@4 xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view -@4 xx#tlen.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view -@4 xx#tlen.tmp.bam.cram.bam > 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=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view -@4 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 -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 -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=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view -@4 xx#tlen2.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view -@4 xx#tlen2.tmp.bam.cram.bam > 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=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view -@4 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view -@4 xx#triplet.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view -@4 xx#triplet.tmp.bam.cram.bam > 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=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view -@4 xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -@4 -S -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 -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=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
test_vcf_api:
/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/Vnp1OBG3Ea/test-vcf-api.bcf
.. ok
test_vcf_sweep:
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/Vnp1OBG3Ea/test-vcf-api.bcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -ch /<<PKGBUILDDIR>>/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatcols.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/noroundtrip.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatmissing.vcf
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 674403825
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 1201167758
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 1392973243
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 940678833
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 1383756915
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 1135139376
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 793110104
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 939155168
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 607931245
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/Vnp1OBG3Ea -s 630120218
.. ok
test_command:
/<<PKGBUILDDIR>>/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/Vnp1OBG3Ea/headernul0.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/Vnp1OBG3Ea/headernul1.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/Vnp1OBG3Ea/headernul678.bam
.. ok
test_rebgzip:
/<<PKGBUILDDIR>>/bgzip -I /<<PKGBUILDDIR>>/test/bgziptest.txt.gz.gzi -c -g /<<PKGBUILDDIR>>/test/bgziptest.txt
.. ok
test-logging:
/<<PKGBUILDDIR>>/test/test-logging.pl
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -r -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02-r.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp-a.sam -o -
.. ok
Number of tests:
total .. 97
passed .. 97
failed .. 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/tabix.substvars
rm -fr -- debian/.debhelper/generated/libhts2/ debian/libhts2/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
rm /<<PKGBUILDDIR>>/test/${binary} ; \
done
dh_auto_install -- \
prefix=/usr \
libdir=/usr/lib/arm-linux-gnueabihf \
PACKAGE_VERSION="1.9-8"
install -d /<<PKGBUILDDIR>>/debian/tmp
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/arm-linux-gnueabihf PACKAGE_VERSION=1.9-8
make[2]: Entering directory '/<<PKGBUILDDIR>>'
echo '#define HTS_VERSION "1.9-8"' > version.h
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/include /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
if test -n ""; then mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp; fi
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.9-8#g' htslib.pc.tmp > /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
gcc -shared -Wl,-soname,libhts.so.2 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.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_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
ln -sf libhts.so libhts.so.2
install -p -m 644 libhts.so /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8
ln -sf libhts.so.1.9-8 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.9-8 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.2
install -p bgzip htsfile tabix /<<PKGBUILDDIR>>/debian/tmp/usr/bin
if test -n ""; then install -p /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 htslib/*.h /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# 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 '/<<PKGBUILDDIR>>'
dh_install -a
install -d debian/libhts2/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.2 debian/libhts2/usr/lib/arm-linux-gnueabihf/
install -d debian/.debhelper/generated/libhts2
install -d debian/libhts-dev/usr/include
cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/
install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/
install -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/
install -d debian/libhts-dev/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/libhts-dev/usr/share/man/man5/
install -d debian/.debhelper/generated/libhts-dev
install -d debian/.debhelper/generated/libhts-private-dev
install -d debian/.debhelper/generated/htslib-test
install -d debian/tabix/usr/bin
cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/
install -d debian/.debhelper/generated/tabix
dh_installdocs -a
install -d debian/libhts2/usr/share/doc/libhts2
install -p -m0644 debian/copyright debian/libhts2/usr/share/doc/libhts2/copyright
install -d debian/libhts-dev/usr/share/doc/libhts-dev
cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev
chown -R 0:0 debian/libhts-dev/usr/share/doc
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 -d debian/tabix/usr/share/doc/tabix
install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright
rm -f debian/libhts-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
install -p -m0644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian
install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog
install -p -m0644 debian/changelog debian/libhts2/usr/share/doc/libhts2/changelog.Debian
install -p -m0644 NEWS debian/libhts2/usr/share/doc/libhts2/changelog
install -p -m0644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian
install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
install -d debian/tabix/usr/share/man/man1/
install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1
install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1
man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/faidx.5 > debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new
man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/sam.5 > debian/libhts-dev/usr/share/man/man5/sam.5.dh-new
man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/htsfile.1 > debian/tabix/usr/share/man/man1/htsfile.1.dh-new
mv debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new debian/libhts-dev/usr/share/man/man5/faidx.5
man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/vcf.5 > debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new
mv debian/libhts-dev/usr/share/man/man5/sam.5.dh-new debian/libhts-dev/usr/share/man/man5/sam.5
man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/tabix.1 > debian/tabix/usr/share/man/man1/tabix.1.dh-new
mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1
chmod 0644 -- debian/tabix/usr/share/man/man1/htsfile.1
mv debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new debian/libhts-dev/usr/share/man/man5/vcf.5
chmod 0644 -- debian/libhts-dev/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/vcf.5
mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1
chmod 0644 -- debian/libhts-dev/usr/share/man/man5/sam.5 debian/tabix/usr/share/man/man1/tabix.1
dh_perl -a
dh_link -a
rm -f debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
ln -s libhts.so.1.9-8 debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.2
rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
ln -s libhts.so.1.9-8 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
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 -a
dh_compress -a
cd debian/libhts2
cd debian/libhts-dev
cd debian/tabix
chmod a-x usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
gzip -9nf usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian
chmod a-x usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
gzip -9nf usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5
gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
dh_fixperms -a
find debian/libhts2 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/tabix -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts2 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts2/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts2/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts2/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev/usr/share/man debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts2/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing -a
dh_strip -a
strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.a
install -d debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/42
objcopy --only-keep-debug --compress-debug-sections debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8 debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/42/88cd3d42021d56da410bbf5d36606bababb1b3.debug
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/7f
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/7f/53f83528a615f9f91fea4bff5592cc423294f8.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/7f/53f83528a615f9f91fea4bff5592cc423294f8.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/7f/53f83528a615f9f91fea4bff5592cc423294f8.debug
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip
objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/7f/53f83528a615f9f91fea4bff5592cc423294f8.debug debian/tabix/usr/bin/bgzip
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/kfunc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/knetfile.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/kstring.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/bcf_sr_sort.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/bgzf.o: plugin needed to handle lto object
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/dc
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/dc/2fd34be4c5cad025ba76411f9561f3968eb107.debug
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/errmod.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/faidx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hfile.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hfile_net.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hts.o: plugin needed to handle lto object
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/42/88cd3d42021d56da410bbf5d36606bababb1b3.debug
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/42/88cd3d42021d56da410bbf5d36606bababb1b3.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hts_os.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/md5.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/multipart.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/probaln.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/realn.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/regidx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/sam.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/synced_bcf_reader.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/vcf_sweep.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/tbx.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/textutils.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/thread_pool.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/vcf.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/vcfutils.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_codecs.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_decode.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_encode.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_external.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_index.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_io.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_samtools.o: plugin needed to handle lto object
objcopy --add-gnu-debuglink debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/42/88cd3d42021d56da410bbf5d36606bababb1b3.debug debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/cram_stats.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/files.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/mFILE.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/open_trace_file.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/pooled_alloc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/rANS_static.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/sam_header.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/string_alloc.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hfile_libcurl.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hfile_gcs.o: plugin needed to handle lto object
strip: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/stmoWPvR/hfile_s3.o: plugin needed to handle lto object
install -d debian/.debhelper/libhts2/dbgsym-root/usr/share/doc
ln -s libhts2 debian/.debhelper/libhts2/dbgsym-root/usr/share/doc/libhts2-dbgsym
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/dc/2fd34be4c5cad025ba76411f9561f3968eb107.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/dc/2fd34be4c5cad025ba76411f9561f3968eb107.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/dc/2fd34be4c5cad025ba76411f9561f3968eb107.debug debian/tabix/usr/bin/htsfile
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c4
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c4/1a5e678cbd0ca19af492717418b801884de8a2.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c4/1a5e678cbd0ca19af492717418b801884de8a2.debug
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c4/1a5e678cbd0ca19af492717418b801884de8a2.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/c4/1a5e678cbd0ca19af492717418b801884de8a2.debug debian/tabix/usr/bin/tabix
install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc
ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym
dh_makeshlibs -a
rm -f debian/libhts2/DEBIAN/shlibs
install -d debian/libhts2/DEBIAN
echo "libhts 2 libhts2" >> debian/libhts2/DEBIAN/shlibs
chmod 0644 -- debian/libhts2/DEBIAN/shlibs
chown 0:0 -- debian/libhts2/DEBIAN/shlibs
dpkg-gensymbols -plibhts2 -Idebian/libhts2.symbols -Pdebian/libhts2 -edebian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8
mv debian/.debhelper/generated/libhts2/triggers.new debian/.debhelper/generated/libhts2/triggers
rm -f debian/libhts-dev/DEBIAN/shlibs
rm -f debian/tabix/DEBIAN/shlibs
dh_shlibdeps -a
dpkg-shlibdeps -Tdebian/libhts2.substvars debian/libhts2/usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8
install -d debian/tabix/DEBIAN
dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip were not linked against libm.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -p -m0644 debian/.debhelper/generated/libhts2/triggers debian/libhts2/DEBIAN/triggers
install -d debian/libhts-dev/DEBIAN
dh_gencontrol -a
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 -Pdebian/libhts-dev
echo misc:Depends= >> debian/libhts2.substvars
echo misc:Pre-Depends= >> debian/libhts2.substvars
install -d debian/.debhelper/libhts2/dbgsym-root/DEBIAN
dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/.debhelper/libhts2/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=libhts2-dbgsym "-DDepends=libhts2 (= \${binary:Version})" "-DDescription=debug symbols for libhts2" -DBuild-Ids=4288cd3d42021d56da410bbf5d36606bababb1b3 -DSection=debug -UReplaces -UBreaks
echo misc:Depends= >> debian/tabix.substvars
echo misc:Pre-Depends= >> debian/tabix.substvars
install -d debian/.debhelper/tabix/dbgsym-root/DEBIAN
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=7f53f83528a615f9f91fea4bff5592cc423294f8 c41a5e678cbd0ca19af492717418b801884de8a2 dc2fd34be4c5cad025ba76411f9561f3968eb107" -DSection=debug -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
chmod 0644 -- debian/libhts-dev/DEBIAN/control
chown 0:0 -- debian/libhts-dev/DEBIAN/control
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/libhts2
chmod 0644 -- debian/tabix/DEBIAN/control
chown 0:0 -- debian/tabix/DEBIAN/control
chmod 0644 -- debian/libhts2/DEBIAN/control
chown 0:0 -- debian/libhts2/DEBIAN/control
dh_md5sums -a
cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libhts2 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/tabix/DEBIAN/md5sums
chown 0:0 -- debian/tabix/DEBIAN/md5sums
chmod 0644 -- debian/libhts2/DEBIAN/md5sums
chown 0:0 -- debian/libhts2/DEBIAN/md5sums
cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/.debhelper/libhts2/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
chown 0:0 -- debian/libhts-dev/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/libhts2 ..
dpkg-deb --build debian/libhts-dev ..
dpkg-deb --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.9-8_armhf.deb'.
dpkg-deb: building package 'libhts2' in '../libhts2_1.9-8_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.9-8_armhf.deb'.
dpkg-deb --build debian/.debhelper/libhts2/dbgsym-root ..
dpkg-deb: building package 'libhts2-dbgsym' in '../libhts2-dbgsym_1.9-8_armhf.deb'.
dpkg-deb --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.9-8_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../htslib_1.9-8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-01-05T05:02:56Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.9-8_armhf.changes:
---------------------------
Format: 1.8
Date: Mon, 31 Dec 2018 07:08:13 -0800
Source: htslib
Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix
Architecture: armhf
Version: 1.9-8
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
htslib-test - Test data for HTSlib
libhts-dev - development files for the HTSlib
libhts-private-dev - private development files for the HTSlib (use with care)
libhts2 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Changes:
htslib (1.9-8) unstable; urgency=medium
.
* Disable optimization on ppc64el to unblock this and many other packages
migration to testing.
Checksums-Sha1:
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fa28dc6edfd80c8b3bafb1f16fda0cec8a529b21f3e7950e6cefd55f87f608ab 4279932 libhts-dev_1.9-8_armhf.deb
9c2424af88af3bd64cb64c9c749c027d1df5df33d6f5277acf1f906763010f28 217268 libhts2-dbgsym_1.9-8_armhf.deb
f3830fdd1a0332bd894a031229fea1398592f008956e11a1dc2eb003f0ac6f6e 254184 libhts2_1.9-8_armhf.deb
278791516245264ef5ba420a48d78abee75dc3c885758c6a0b20a90310d72be4 512076 tabix-dbgsym_1.9-8_armhf.deb
3b2e15bac761338ca662b77f107d6e06f88df0a315a8b6e3ba78743784f8c9ed 240448 tabix_1.9-8_armhf.deb
Files:
5022513dcccfd7ec790c89c0ae2e8ca6 6020 science optional htslib_1.9-8_armhf.buildinfo
aede8bf82aebea1532f09744edb6e425 4279932 libdevel optional libhts-dev_1.9-8_armhf.deb
df6e78215b2a96847c2ef75220ef7a17 217268 debug optional libhts2-dbgsym_1.9-8_armhf.deb
18c05efe5e83d3417201b7de8bfd9e31 254184 libs optional libhts2_1.9-8_armhf.deb
0eec6c21132653d0f4e5117818c51296 512076 debug optional tabix-dbgsym_1.9-8_armhf.deb
a9d24de099bc9d076d606fdc04cb4506 240448 science optional tabix_1.9-8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts-dev_1.9-8_armhf.deb
--------------------------
new Debian package, version 2.0.
size 4279932 bytes: control archive=1864 bytes.
1044 bytes, 24 lines control
2259 bytes, 35 lines md5sums
Package: libhts-dev
Source: htslib
Version: 1.9-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5127
Depends: libhts2 (= 1.9-8), 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.
drwxr-xr-x root/root 0 2018-12-31 15:08 ./
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/include/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/include/htslib/
-rw-r--r-- root/root 14797 2018-07-18 08:33 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 15393 2018-07-18 08:33 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 8972 2018-07-18 08:33 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 10077 2018-07-18 08:33 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 30459 2018-07-18 08:33 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 3336 2018-07-18 08:33 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 11446 2018-07-18 08:33 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root 3898 2018-07-18 08:33 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root 1996 2018-07-18 08:33 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root 4195 2018-07-18 08:33 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2716 2018-07-18 08:33 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 21540 2018-07-18 08:33 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 3990 2018-07-18 08:33 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5086 2018-07-18 08:33 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 2850 2018-07-18 08:33 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 9139 2018-07-18 08:33 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 10567 2018-07-18 08:33 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 7012 2018-07-18 08:33 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 5834 2018-07-18 08:33 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 29580 2018-07-18 08:33 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 14954 2018-07-18 08:33 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 3118 2018-07-18 08:33 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 9386 2018-07-18 08:33 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root 43671 2018-07-18 08:33 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1602 2018-07-18 08:33 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4819 2018-07-18 08:33 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 4915412 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root 0 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.9-8
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 565 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 401 2018-12-11 01:59 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root 4093 2018-12-31 15:08 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 8097 2018-07-18 08:33 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5762 2018-12-11 02:07 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/man/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/man/man5/
-rw-r--r-- root/root 2452 2018-12-31 15:08 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root 1535 2018-12-31 15:08 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1854 2018-12-31 15:08 ./usr/share/man/man5/vcf.5.gz
libhts2-dbgsym_1.9-8_armhf.deb
------------------------------
new Debian package, version 2.0.
size 217268 bytes: control archive=548 bytes.
382 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libhts2-dbgsym
Source: htslib
Version: 1.9-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 308
Depends: libhts2 (= 1.9-8)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libhts2
Build-Ids: 4288cd3d42021d56da410bbf5d36606bababb1b3
drwxr-xr-x root/root 0 2018-12-31 15:08 ./
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/.build-id/42/
-rw-r--r-- root/root 304880 2018-12-31 15:08 ./usr/lib/debug/.build-id/42/88cd3d42021d56da410bbf5d36606bababb1b3.debug
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-12-31 15:08 ./usr/share/doc/libhts2-dbgsym -> libhts2
libhts2_1.9-8_armhf.deb
-----------------------
new Debian package, version 2.0.
size 254184 bytes: control archive=4792 bytes.
1102 bytes, 22 lines control
289 bytes, 4 lines md5sums
17 bytes, 1 lines shlibs
20119 bytes, 747 lines symbols
63 bytes, 2 lines triggers
Package: libhts2
Source: htslib
Version: 1.9-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 623
Depends: libbz2-1.0, libc6 (>= 2.23), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
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 2018-12-31 15:08 ./
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 587180 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.9-8
lrwxrwxrwx root/root 0 2018-12-31 15:08 ./usr/lib/arm-linux-gnueabihf/libhts.so.2 -> libhts.so.1.9-8
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/libhts2/
-rw-r--r-- root/root 4093 2018-12-31 15:08 ./usr/share/doc/libhts2/changelog.Debian.gz
-rw-r--r-- root/root 8097 2018-07-18 08:33 ./usr/share/doc/libhts2/changelog.gz
-rw-r--r-- root/root 5762 2018-12-11 02:07 ./usr/share/doc/libhts2/copyright
tabix-dbgsym_1.9-8_armhf.deb
----------------------------
new Debian package, version 2.0.
size 512076 bytes: control archive=652 bytes.
441 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: tabix-dbgsym
Source: htslib
Version: 1.9-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 680
Depends: tabix (= 1.9-8)
Section: debug
Priority: optional
Description: debug symbols for tabix
Build-Ids: 7f53f83528a615f9f91fea4bff5592cc423294f8 c41a5e678cbd0ca19af492717418b801884de8a2 dc2fd34be4c5cad025ba76411f9561f3968eb107
drwxr-xr-x root/root 0 2018-12-31 15:08 ./
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/.build-id/7f/
-rw-r--r-- root/root 197356 2018-12-31 15:08 ./usr/lib/debug/.build-id/7f/53f83528a615f9f91fea4bff5592cc423294f8.debug
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root 245096 2018-12-31 15:08 ./usr/lib/debug/.build-id/c4/1a5e678cbd0ca19af492717418b801884de8a2.debug
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/lib/debug/.build-id/dc/
-rw-r--r-- root/root 240276 2018-12-31 15:08 ./usr/lib/debug/.build-id/dc/2fd34be4c5cad025ba76411f9561f3968eb107.debug
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-12-31 15:08 ./usr/share/doc/tabix-dbgsym -> tabix
tabix_1.9-8_armhf.deb
---------------------
new Debian package, version 2.0.
size 240448 bytes: control archive=1096 bytes.
941 bytes, 19 lines control
481 bytes, 8 lines md5sums
Package: tabix
Source: htslib
Version: 1.9-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 803
Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0)
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 version of tabix is built from the HTSlib source.
drwxr-xr-x root/root 0 2018-12-31 15:08 ./
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/bin/
-rwxr-xr-x root/root 83412 2018-12-31 15:08 ./usr/bin/bgzip
-rwxr-xr-x root/root 353756 2018-12-31 15:08 ./usr/bin/htsfile
-rwxr-xr-x root/root 349652 2018-12-31 15:08 ./usr/bin/tabix
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/doc/tabix/
-rw-r--r-- root/root 4093 2018-12-31 15:08 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root 8097 2018-07-18 08:33 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root 5762 2018-12-11 02:07 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/man/
drwxr-xr-x root/root 0 2018-12-31 15:08 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2018-12-31 15:08 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
-rw-r--r-- root/root 1700 2018-12-31 15:08 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root 2770 2018-12-31 15:08 ./usr/share/man/man1/tabix.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 47680
Build-Time: 382
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 119
Job: htslib_1.9-8
Machine Architecture: armhf
Package: htslib
Package-Time: 518
Source-Version: 1.9-8
Space: 47680
Status: successful
Version: 1.9-8
--------------------------------------------------------------------------------
Finished at 2019-01-05T05:02:56Z
Build needed 00:08:38, 47680k disk space