htslib →
1.13+ds-2 →
armhf → 2021-09-02 06:23:32
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| htslib 1.13+ds-2 (armhf) Thu, 02 Sep 2021 05:38:58 +0000 |
+==============================================================================+
Package: htslib
Version: 1.13+ds-2
Source Version: 1.13+ds-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-7c564f77-cd53-4554-8c00-9113ba189f99' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.7 MB in 29s (888 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 1390 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main htslib 1.13+ds-2 (dsc) [2446 B]
Get:2 http://172.17.0.1/private bookworm-staging/main htslib 1.13+ds-2 (tar) [1370 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main htslib 1.13+ds-2 (diff) [17.5 kB]
Fetched 1390 kB in 1s (1722 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-0fOSEP/htslib-1.13+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-0fOSEP' 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-kGivsW/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-kGivsW/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-kGivsW/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-kGivsW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2905 B/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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 52 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-kGivsW/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 (14.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12488 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-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0)
Filtered Build-Depends: debhelper-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0)
dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<<BUILDDIR>>/resolver-kGivsW/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-kGivsW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Sources [556 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ Packages [634 B]
Fetched 2523 B in 1s (3474 B/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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhtscodecs-dev
libhtscodecs2 libicu67 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc 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 ca-certificates libarchive-cpio-perl
publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhtscodecs-dev
libhtscodecs2 libicu67 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl-dev
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-htslib-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
libssl1.1
1 upgraded, 48 newly installed, 0 to remove and 51 not upgraded.
Need to get 24.7 MB of archives.
After this operation, 79.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-kGivsW/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libssl1.1 armhf 1.1.1l-1 [1276 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.1 [192 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.1 [1056 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf dh-exec armhf 0.23.4 [25.7 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.9.0-3 [151 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.7-2 [44.1 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.7-2 [40.5 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-2 [49.7 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs-dev armhf 1.1.1-2 [2568 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libssl-dev armhf 1.1.1l-1 [1581 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libdeflate-dev:armhf (1.7-2) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../37-libhtscodecs2_1.1.1-2_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.1.1-2) ...
Selecting previously unselected package libhtscodecs-dev:armhf.
Preparing to unpack .../38-libhtscodecs-dev_1.1.1-2_armhf.deb ...
Unpacking libhtscodecs-dev:armhf (1.1.1-2) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../39-liblzma-dev_5.2.5-2_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-2) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../40-libssl-dev_1.1.1l-1_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1l-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../41-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-htslib-dummy.
Preparing to unpack .../42-sbuild-build-depends-htslib-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-2) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-2) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libhtscodecs-dev:armhf (1.1.1-2) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libssl-dev:armhf (1.1.1l-1) ...
Setting up autopoint (0.21-4) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-3) ...
Setting up libdeflate-dev:armhf (1.7-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.7) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.1) ...
Setting up dh-exec (0.23.4) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.5.1 debianutils_4.11.2 dh-autoreconf_20 dh-exec_0.23.4 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libhtscodecs-dev_1.1.1-2 libhtscodecs2_1.1.1-2 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl-dev_1.1.1l-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.17 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.YvCe8KcV/trustedkeys.kbx': General error
gpgv: Signature made Fri Aug 27 20:28:31 2021 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./htslib_1.13+ds-2.dsc
dpkg-source: info: extracting htslib in /<<BUILDDIR>>/htslib-1.13+ds
dpkg-source: info: unpacking htslib_1.13+ds.orig.tar.bz2
dpkg-source: info: unpacking htslib_1.13+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_git_version
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying fPIC.patch
dpkg-source: info: applying testShebang.patch
dpkg-source: info: applying fix_float_precision
dpkg-source: info: applying cram_to_bam_export.patch
dpkg-source: info: applying disable_plugin_loading_test.patch
Check disc 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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-7c564f77-cd53-4554-8c00-9113ba189f99
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.13+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.13+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_auto_clean
install -d /<<BUILDDIR>>/htslib-1.13\+ds/debian/.debhelper/generated/_source/home
make -j4 distclean
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt
rm -f libhts.so libhts.so.*
rm -rf htscodecs/tests/test.out
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h
rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico
rm -f hts-object-files
rm -f htscodecs/tests/*.o
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_kfunc test/test_kstring test/test_realn test/test-regidx test/test_str2int test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7
rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk
rm -rf autom4te.cache
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -rf test_backup/
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
rm -fr -- debian/libhts3/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary-arch
dh binary-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 '/<<BUILDDIR>>/htslib-1.13+ds'
# create clean copy of test dir
cp -a test test_backup
# to help with cross building, otherwise MMAP might get turned off
export ac_cv_func_mmap_fixed_mapped=yes && autoconf && \
dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir='/htslib' --with-external-htscodecs --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:'
install -d /<<BUILDDIR>>/htslib-1.13\+ds/debian/.debhelper/generated/_source/home
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether 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 pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
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... (cached) yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing dlsym... -ldl
checking whether the compiler accepts -rdynamic... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for htscodecs/rANS_static4x16.h... yes
checking for rans_compress_bound_4x16 in -lhtscodecs... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
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
config.status: linking htscodecs_external.mk to htscodecs.mk
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="1.13+ds" \
libdir=/usr/lib/arm-linux-gnueabihf
make -j4 "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.13\+ds libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.13+ds"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS "-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2"' >> config_vars.h
echo '#define HTS_CFLAGS "-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl "' >> config_vars.h
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:\" -c -o plugin.o plugin.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:\" -fPIC -c -o plugin.pico plugin.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -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 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o
ranlib libhts.a
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
ln -sf libhts.so libhts.so.3
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lcurl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lcrypto -lpthread
gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -ldl -lcrypto -lcurl -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_auto_test -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="1.13+ds" \
libdir=/usr/lib/arm-linux-gnueabihf \
|| \
if find . -name "FAIL*" > /dev/null ; then \
for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \
fi
make -j4 test VERBOSE=1 "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.13\+ds libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
test/hts_endian
test/test_expr
test/test_kfunc
test/test_kstring
test/test_str2int
test/fieldarith test/fieldarith.sam
test/hfile
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so
test/test_bgzf test/bgziptest.txt
test/test-parse-reg -t test/colons.bam
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead
Expected error: [E::hts_parse_region] Mismatching braces in "{chr1"
Expected error: [E::hts_parse_region] Unexpected string "x" after region
Expected error: [E::hts_parse_region] Unexpected string "y" after region
Expected error: [E::hts_parse_region] Unexpected string "chr3" after region
cd test/sam_filter && ./filter.sh filter.tst
Testing sam_filter...
PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam
PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam
PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam
PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam
PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam
PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@'
PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@'
PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@'
PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@'
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/tabix && ./test-tabix.sh tabix.tst
Testing tabix...
PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero)
PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz
PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz
PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz
PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190
PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/mpileup && ./test-pileup.sh mpileup.tst
Testing (m)pileup...
PASS : $pileup mp_D.sam
PASS : $pileup -m mp_D.sam
PASS : $pileup mp_DI.sam
PASS : $pileup -m mp_DI.sam
PASS : $pileup mp_I.sam
PASS : $pileup -m mp_I.sam
PASS : $pileup mp_P.sam
PASS : $pileup -m mp_P.sam
PASS : $pileup mp_ID.sam
PASS : $pileup -m mp_ID.sam
PASS : $pileup mp_N.sam
PASS : $pileup -m mp_N.sam
PASS : $pileup mp_N2.sam
PASS : $pileup -m mp_N2.sam
PASS : $pileup c1#pad1.sam
PASS : $pileup -m c1#pad1.sam
PASS : $pileup c1#pad2.sam
PASS : $pileup -m c1#pad2.sam
PASS : $pileup c1#pad3.sam
PASS : $pileup -m c1#pad3.sam
PASS : $pileup -m small.bam
Expected passes: 21
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
cd test/fastq && ./test-fastq.sh
Testing fastq support
PASS : $tview minimal.fq
PASS : $tview minimal.fa
PASS : $tview multiline.fq
PASS : $tview multiline.fa
PASS : $tview single.fq
PASS : $tview single.fa
PASS : $tview -i fastq_aux single.fq
PASS : $tview -i fastq_aux single.fa
PASS : $tview interleaved.fq
PASS : $tview interleaved.fa
PASS : $tview -i fastq_aux interleaved.fq
PASS : $tview -i fastq_aux interleaved.fa
PASS : $tview -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_casava filter_casava.fq
PASS : $tview -i fastq_casava filter_casava.fa
PASS : $tview -i fastq_aux r1.fq
PASS : $tview -i fastq_aux r2.fq
PASS : $tview -i fastq_aux r1.fa
PASS : $tview -i fastq_aux r2.fa
PASS : $tview -f minimal.sam
PASS : $tview -F minimal.sam
PASS : $tview -f -o fastq_aux single_aux.sam
PASS : $tview -F -o fastq_aux single_aux.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -f -o fastq_casava inter_casava.sam
PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -F -o fastq_casava inter_casava.sam
PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -f -o fastq_casava filter_casava.sam
PASS : $tview -F -o fastq_casava filter_casava.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam
Expected passes: 38
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:-}
bgzip round-trip no threads: .. ok
bgzip -b no threads: .. ok
bgzip -b -I no threads: .. ok
bgzip round-trip 4 threads: .. ok
bgzip -b 4 threads: .. ok
bgzip -b -I 4 threads: .. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -b -m 14 -x /tmp/cF3txzCBU3/index.bam.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -b -m 0 -x /tmp/cF3txzCBU3/index.bam.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 14 -x /tmp/cF3txzCBU3/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 0 -x /tmp/cF3txzCBU3/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 14 -x /tmp/cF3txzCBU3/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 0 -x /tmp/cF3txzCBU3/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -C -x /tmp/cF3txzCBU3/index.cram.crai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index /tmp/cF3txzCBU3/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -b -m 14 -x /tmp/cF3txzCBU3/index.bcf.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/cF3txzCBU3/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 14 -x /tmp/cF3txzCBU3/index.vcf.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -l 0 -z -m 0 -x /tmp/cF3txzCBU3/index.vcf.gz.tbi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -t /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/tabix /tmp/cF3txzCBU3/index.vcf.gz##idx##/tmp/cF3txzCBU3/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/cF3txzCBU3/index.bam.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/cF3txzCBU3/index.bam.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/cF3txzCBU3/index.bam
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/cF3txzCBU3/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/cF3txzCBU3/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/cF3txzCBU3/index.sam.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/cF3txzCBU3/index.sam.gz.bai /<<BUILDDIR>>/htslib-1.13+ds/test/index_dos.sam > /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -b /tmp/cF3txzCBU3/index.sam.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -C -x /tmp/cF3txzCBU3/index.cram.crai /<<BUILDDIR>>/htslib-1.13+ds/test/index.sam > /tmp/cF3txzCBU3/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index /tmp/cF3txzCBU3/index.cram
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/cF3txzCBU3/index.bcf.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/cF3txzCBU3/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.bcf
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/cF3txzCBU3/index.vcf.gz.csi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/cF3txzCBU3/index.vcf.gz.tbi /<<BUILDDIR>>/htslib-1.13+ds/test/index.vcf > /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -t /tmp/cF3txzCBU3/index.vcf.gz
.. ok
test_index:
/<<BUILDDIR>>/htslib-1.13+ds/tabix /tmp/cF3txzCBU3/index.vcf.gz##idx##/tmp/cF3txzCBU3/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_view testing multi-ref CRAM modes:
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing multi-ref CRAM modes:
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -S -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 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=3.1 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t auxf.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=4.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t auxf.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.1 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=4.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t c2.fa -S -l7 -C -o VERSION=3.1 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=3.1 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c2.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=4.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t c2.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.1 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=4.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t md.fa -S -l7 -C -o VERSION=3.1 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -t md.fa -C -o VERSION=3.1 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t md.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -t md.fa -C -o VERSION=4.0 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t md.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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#MD.sam, ref xx.fa:
./test_view -S -b xx#MD.sam > xx#MD.tmp.bam
./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD.sam > xx#MD.tmp.cram
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -S -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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_
./test_view -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -S -l7 -C -o VERSION=3.1 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.1 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view 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 -S -l7 -C -o VERSION=4.0 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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 -S -l7 -C -o VERSION=4.0 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=4.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=4.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
test_view testing region queries:
./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -@4 -S -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 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -C -o VERSION=3.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -@4 -t auxf.fa -C -o VERSION=3.1 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t auxf.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o fast auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o normal auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o small auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
./test_view -@4 -t auxf.fa -C -o VERSION=4.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -@4 -t auxf.fa -C -o VERSION=4.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t auxf.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=3.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o normal c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o small c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o archive c1#bounds.sam > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=4.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=3.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o normal c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o small c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o archive c1#clip.sam > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=4.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=3.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o normal c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o small c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o archive c1#noseq.sam > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=4.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=3.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o small c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad1.sam > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=4.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=3.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o normal c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o small c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o archive c1#pad2.sam > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=4.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o fast c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o normal c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o small c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=3.1 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=3.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=3.1 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o normal c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o small c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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 -S -l7 -C -o VERSION=4.0 -o archive c1#unknown.sam > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D c1#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=4.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -@4 -t c1.fa -C -o VERSION=4.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c1.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t c2.fa -S -l7 -C -o VERSION=3.1 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=3.1 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=3.1 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=3.1 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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=3.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -@4 -t c2.fa -C -o VERSION=3.1 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c2.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=4.0 -o normal c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=4.0 -o small c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=4.0 -o archive c2#pad.sam > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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=4.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -@4 -t c2.fa -C -o VERSION=4.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t c2.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#1.sam > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#1000.tmp.cram > ce#1000.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#2.sam > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#5b.sam > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#tag_padded.sam > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap.sam > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap1.sam > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=3.1 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=3.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=3.1 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o normal ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o small ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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 -S -l7 -C -o VERSION=4.0 -o archive ce#unmap2.sam > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D ce#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=4.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -@4 -t ce.fa -C -o VERSION=4.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t ce.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t md.fa -S -l7 -C -o VERSION=3.1 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=3.1 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=3.1 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=3.1 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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=3.1 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -@4 -t md.fa -C -o VERSION=3.1 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t md.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=4.0 -o normal md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=4.0 -o small md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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 -S -l7 -C -o VERSION=4.0 -o archive md#1.sam > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D 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=4.0 md#1.tmp.bam > md#1.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 md#1.tmp.cram > md#1.tmp.cram.cram
./test_view -@4 -t md.fa -C -o VERSION=4.0 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t md.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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 -S -l7 -C -o VERSION=3.1 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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 -S -l7 -C -o VERSION=3.1 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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 -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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=3.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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 -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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 -S -l7 -C -o VERSION=4.0 -o small xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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 -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux2.sam > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#large_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=4.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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#MD.sam, ref xx.fa:
./test_view -@4 -S -b xx#MD.sam > xx#MD.tmp.bam
./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD.sam > xx#MD.tmp.cram
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam
./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram > xx#MD.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_view testing xx#MD2.sam, ref xx.fa:
./test_view -@4 -S -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD2.sam > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam
./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -nomd xx#MD2.sam xx#MD2.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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=3.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o normal xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o small xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o archive xx#minimal.sam > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=4.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=3.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o normal xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o small xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o archive xx#repeated.sam > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=4.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=3.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o normal xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o small xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o archive xx#rg.sam > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=4.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=3.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o normal xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o small xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o archive xx#tlen2.sam > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=4.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=3.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o normal xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o small xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o archive xx#triplet.sam > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=4.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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_
./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=3.1 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=3.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=3.1 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 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 -S -l7 -C -o VERSION=4.0 -o fast xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o normal xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o small xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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 -S -l7 -C -o VERSION=4.0 -o archive xx#unsorted.sam > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -D xx#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=4.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -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=3.0 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -@4 -t xx.fa -C -o VERSION=4.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 -t xx.fa -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
test_view testing region queries:
./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
./compare_sam.pl range.tmp range.out
.. ok
test_view testing BAM files with absent @SQ lines:
./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok
test_view testing large (> 2Gbases) positions:
./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok
./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok
test_MD testing xx#MD.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_
Checking for MD/NM in xx#MD.sam
./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_
.. ok
test_MD testing xx#MD2.sam, ref xx.fa:
./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_
./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok
test_vcf_api:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-vcf-api /tmp/cF3txzCBU3/test-vcf-api.bcf
[W::bcf_record_check] Bad BCF record at 1:1: No REF allele
[E::bcf_index_build3] TBI indices for BCF files are not supported
[E::idx_find_and_load] Could not retrieve index file for '/tmp/cF3txzCBU3/test-vcf-api.bcf'
.. ok
test_bcf2vcf:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view /<<BUILDDIR>>/htslib-1.13+ds/test/tabix/vcf_file.bcf
.. ok
test_vcf_sweep:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-vcf-sweep /tmp/cF3txzCBU3/test-vcf-api.bcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -ch /<<BUILDDIR>>/htslib-1.13+ds/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/formatcols.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/noroundtrip.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/formatmissing.vcf
.. ok
test_vcf_various:
/<<BUILDDIR>>/htslib-1.13+ds/htsfile -c /<<BUILDDIR>>/htslib-1.13+ds/test/vcf_meta_meta.vcf
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 239779847
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 429448782
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 740220163
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 340986452
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 234109621
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 364002924
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 700186590
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 150554200
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 535459545
.. ok
test-bcf-sr:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-sr.pl -t /tmp/cF3txzCBU3 -s 785863375
.. ok
test_command:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -t ce.fa -C /tmp/cF3txzCBU3/headernul0.bam
.. ok
test_convert_padded_header:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -t ce.fa -C /tmp/cF3txzCBU3/headernul1.bam
.. ok
test_convert_padded_header:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_view -t ce.fa -C /tmp/cF3txzCBU3/headernul678.bam
.. ok
test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
/<<BUILDDIR>>/htslib-1.13+ds/bgzip -I /<<BUILDDIR>>/htslib-1.13+ds/test/bgziptest.txt.tmp.gz.gzi -c -g /<<BUILDDIR>>/htslib-1.13+ds/test/bgziptest.txt
.. ok
test-logging:
/<<BUILDDIR>>/htslib-1.13+ds/test/test-logging.pl
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -a -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -a -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -e -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn01.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -e -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -r -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02-r.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -a -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02_exp.sam -o -
.. ok
test_realn:
/<<BUILDDIR>>/htslib-1.13+ds/test/test_realn -f /<<BUILDDIR>>/htslib-1.13+ds/test/realn02.fa -i /<<BUILDDIR>>/htslib-1.13+ds/test/realn02_exp-a.sam -o -
.. ok
Number of tests:
total .. 163
passed .. 163
failed .. 0
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -fr -- /tmp/dh-xdg-rundir-ZoqTvtf9
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
create-stamp debian/debhelper-build-stamp
dh_prep -a
rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/tabix.substvars
rm -fr -- debian/.debhelper/generated/libhts3/ debian/libhts3/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
rm /<<BUILDDIR>>/htslib-1.13+ds/test/${binary} ; \
done
dh_auto_install -- prefix=/usr \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="1.13+ds" \
libdir=/usr/lib/arm-linux-gnueabihf
install -d /<<BUILDDIR>>/htslib-1.13\+ds/debian/tmp
make -j4 install DESTDIR=/<<BUILDDIR>>/htslib-1.13\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/htslib-1.13+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.13\+ds libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
mkdir -p -m 755 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/bin /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/include /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/include/htslib /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man1 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man5 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man7 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig
if test -n "/htslib"; then mkdir -p -m 755 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/htslib; fi
install -p -m 644 libhts.so /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.13+ds
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.13+ds#g' htslib.pc.tmp > /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
chmod 644 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
ln -sf libhts.so.1.13+ds /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.13+ds /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3
install -p bgzip htsfile tabix /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/bin
if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/htslib; fi
install -p -m 644 htslib/*.h /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man5
install -p -m 644 htslib-s3-plugin.7 /<<BUILDDIR>>/htslib-1.13+ds/debian/tmp/usr/share/man/man7
make[2]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
# restore clean copy of test dir before dh_install is run
# This should not be done earlier since dh_auto_install contains some unconditional removals
rm -f -r test
mv test_backup test
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_install -a
install -d debian/libhts3/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a ./debian/tmp/htslib debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3/usr/lib/arm-linux-gnueabihf/
install -d debian/libhts3/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/libhts3/usr/share/man/man5/
install -d debian/.debhelper/generated/libhts3
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/.debhelper/generated/libhts-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
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_installdocs
install -d debian/libhts3/usr/share/doc/libhts3
install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/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
cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev
cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev
chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc
install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright
install -d debian/tabix/usr/share/doc/tabix
install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright
# Fix Perl interpreter path
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
grep: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_installchangelogs NEWS
install -p -m0644 debian/changelog debian/libhts3/usr/share/doc/libhts3/changelog.Debian
install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/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
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
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_installman -a
install -d debian/libhts3/usr/share/man/man7/
install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
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
install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1
man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5
man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/vcf.5 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1
mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1
chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1
mv debian/libhts3/usr/share/man/man5/vcf.5.dh-new debian/libhts3/usr/share/man/man5/vcf.5
mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
chmod 0644 -- debian/libhts3/usr/share/man/man5/vcf.5 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
mv debian/libhts3/usr/share/man/man5/faidx.5.dh-new debian/libhts3/usr/share/man/man5/faidx.5
mv debian/libhts3/usr/share/man/man5/sam.5.dh-new debian/libhts3/usr/share/man/man5/sam.5
chmod 0644 -- debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5
mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1
mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1
chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
dh_perl -a
dh_link -a
rm -f debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
ln -s libhts.so.1.13\+ds debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
ln -s libhts.so.1.13\+ds 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/libhts3
cd debian/libhts-dev
cd debian/tabix
chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian
chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
chmod a-x usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7
gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian
gzip -9nf usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7
gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1
cd '/<<BUILDDIR>>/htslib-1.13+ds'
cd '/<<BUILDDIR>>/htslib-1.13+ds'
cd '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_fixperms
find debian/libhts3 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/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/libhts3/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/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libhts3/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts3 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian -name simple_test_driver.sh -exec chmod +x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_missing
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
# FIXME: No idea why these files are remaining in debian/tmp
rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man
dh_missing
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_dwz -a -a
install -d debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -- debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
install -d debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
dwz: debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13+ds: DWARF compression not beneficial - old size 814185 new size 822903
objcopy --compress-debug-sections debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_strip
make[1]: Entering directory '/<<BUILDDIR>>/htslib-1.13+ds'
# This is apparently important for the interpretation by ldc2 in sambamba
dh_strip -Xlibhts.a
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cc
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cc/4cb3173e95cc96666a8fce3142cf71aaa9fa62.debug
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/86
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/86/4fe6f7503e872b26b4a4a6ede803703a2fa6b9.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cc/4cb3173e95cc96666a8fce3142cf71aaa9fa62.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/cc/4cb3173e95cc96666a8fce3142cf71aaa9fa62.debug debian/tabix/usr/bin/bgzip
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d1
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d1/a58f859fa4ae8fb786365e2a9179e59eb432af.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d1/a58f859fa4ae8fb786365e2a9179e59eb432af.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/d1/a58f859fa4ae8fb786365e2a9179e59eb432af.debug debian/tabix/usr/bin/htsfile
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5c
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5c/ea47cfb2b0c91b0cf0b48087fffe680d959ee7.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/86/4fe6f7503e872b26b4a4a6ede803703a2fa6b9.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/86/4fe6f7503e872b26b4a4a6ede803703a2fa6b9.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/13
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/13/2f581baa26046f646906ccecff608c1166c130.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/13/2f581baa26046f646906ccecff608c1166c130.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/13/2f581baa26046f646906ccecff608c1166c130.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/e8
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/e8/eca28d22b101bc64f7777a6f9c77ace8d3a6db.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/e8/eca28d22b101bc64f7777a6f9c77ace8d3a6db.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/e8/eca28d22b101bc64f7777a6f9c77ace8d3a6db.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/34
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/34/82194cefb6e802a813e62492f90a12883ccc27.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/34/82194cefb6e802a813e62492f90a12883ccc27.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/34/82194cefb6e802a813e62492f90a12883ccc27.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/4c
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/4c/2fc8973a74a94540171f6efd03eed75fc41c0f.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/4c/2fc8973a74a94540171f6efd03eed75fc41c0f.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/4c/2fc8973a74a94540171f6efd03eed75fc41c0f.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/libhts3/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/libhts3/usr/lib/debug
install -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc
ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/5c/ea47cfb2b0c91b0cf0b48087fffe680d959ee7.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/5c/ea47cfb2b0c91b0cf0b48087fffe680d959ee7.debug debian/tabix/usr/bin/tabix
install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/tabix/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug
install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc
ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym
make[1]: Leaving directory '/<<BUILDDIR>>/htslib-1.13+ds'
dh_makeshlibs -a -a
rm -f debian/libhts3/DEBIAN/shlibs
install -d debian/libhts3/DEBIAN
echo "libhts 3 libhts3 (>= 1.13+ds)" >> debian/libhts3/DEBIAN/shlibs
chmod 0644 -- debian/libhts3/DEBIAN/shlibs
dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds
mv debian/.debhelper/generated/libhts3/triggers.new debian/.debhelper/generated/libhts3/triggers
rm -f debian/libhts-dev/DEBIAN/shlibs
rm -f debian/tabix/DEBIAN/shlibs
dh_shlibdeps -a -a
dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.13\+ds debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
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 ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/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/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 -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=5cea47cfb2b0c91b0cf0b48087fffe680d959ee7 cc4cb3173e95cc96666a8fce3142cf71aaa9fa62 d1a58f859fa4ae8fb786365e2a9179e59eb432af" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
echo misc:Depends= >> debian/libhts3.substvars
echo misc:Pre-Depends= >> debian/libhts3.substvars
install -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN
dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/.debhelper/libhts3/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libhts3-dbgsym "-DDepends=libhts3 (= \${binary:Version})" "-DDescription=debug symbols for libhts3" "-DBuild-Ids=132f581baa26046f646906ccecff608c1166c130 3482194cefb6e802a813e62492f90a12883ccc27 4c2fc8973a74a94540171f6efd03eed75fc41c0f 864fe6f7503e872b26b4a4a6ede803703a2fa6b9 e8eca28d22b101bc64f7777a6f9c77ace8d3a6db" -DSection=debug -UReplaces -UBreaks
chmod 0644 -- debian/libhts-dev/DEBIAN/control
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3
chmod 0644 -- debian/tabix/DEBIAN/control
chmod 0644 -- debian/libhts3/DEBIAN/control
dh_md5sums -a
cd debian/libhts3 >/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/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libhts3/DEBIAN/md5sums
chmod 0644 -- debian/tabix/DEBIAN/md5sums
cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/libhts3 ..
dpkg-deb --root-owner-group --build debian/libhts-dev ..
dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.13+ds-2_armhf.deb'.
dpkg-deb: building package 'libhts3' in '../libhts3_1.13+ds-2_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.13+ds-2_armhf.deb'.
dpkg-deb --root-owner-group --build debian/.debhelper/libhts3/dbgsym-root ..
dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.13+ds-2_armhf.deb'.
dpkg-deb --root-owner-group --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.13+ds-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../htslib_1.13+ds-2_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-1.13+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-09-02T06:23:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.13+ds-2_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 27 Aug 2021 22:02:59 +0200
Source: htslib
Binary: libhts-dev libhts3 libhts3-dbgsym tabix tabix-dbgsym
Architecture: armhf
Version: 1.13+ds-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
libhts-dev - development files for the HTSlib
libhts3 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Changes:
htslib (1.13+ds-2) unstable; urgency=medium
.
* d/control: add myself to uploaders
* d/control: libhts-dev breaks samtools (<< 1.13~)
* d/control: refresh libhts-dev Breaks+Replaces
* d/control: libhts-dev breaks ivar (<< 1.3.1~)
Checksums-Sha1:
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1db18b625b60f2544bd1c93606ece950b1ef9537 1107944 libhts3-dbgsym_1.13+ds-2_armhf.deb
f3736508264d0ca8c8afd586e919c905ab1474e3 339224 libhts3_1.13+ds-2_armhf.deb
aeeca953d0fdd0b5ef4c4dd3d69b4ed3df4d6870 1419160 tabix-dbgsym_1.13+ds-2_armhf.deb
a146f6cac54caf9cbbee788141cf7735e800e059 292468 tabix_1.13+ds-2_armhf.deb
Checksums-Sha256:
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c7abfa4283f3900cf9919f25360883e6a5ab3221ca59e87b41608031ff3b6ce5 1107944 libhts3-dbgsym_1.13+ds-2_armhf.deb
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8d1d13a4060699824596327db5103ad919a13160d7fd9a874165e7a8a299d1ee 1419160 tabix-dbgsym_1.13+ds-2_armhf.deb
4214229b319d15ef8ab50bebc46bcc8cfacc8ee8d8f6dab0170fd15cc04528a9 292468 tabix_1.13+ds-2_armhf.deb
Files:
0b81d7e5d68fcdbd026cf84786c8db58 6384 science optional htslib_1.13+ds-2_armhf.buildinfo
6ab8f49628b4283567e3e7cdb2fded2a 4048700 libdevel optional libhts-dev_1.13+ds-2_armhf.deb
3e114072070c54bebcf01ca06c840871 1107944 debug optional libhts3-dbgsym_1.13+ds-2_armhf.deb
7e95c131bcf3eb02a65119bca07f830a 339224 libs optional libhts3_1.13+ds-2_armhf.deb
fdbf6dda6f545e2cfd313ba93a5432ad 1419160 debug optional tabix-dbgsym_1.13+ds-2_armhf.deb
f450f965d57f95fa7b91b09359a3e89f 292468 science optional tabix_1.13+ds-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts-dev_1.13+ds-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 4048700 bytes: control archive=1988 bytes.
1213 bytes, 27 lines control
2353 bytes, 36 lines md5sums
Package: libhts-dev
Source: htslib
Version: 1.13+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5092
Depends: libhts3 (= 1.13+ds-2), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, zlib1g-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/samtools/htslib
Description: development files for the HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
.
This package contains development files for the HTSlib: headers, static
library, manual pages, etc.
.
For compatibility with sambamba, the internal routine cram_to_bam was
exported, hereto adopting a patch found in guix.
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/include/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/include/htslib/
-rw-r--r-- root/root 16081 2020-09-16 10:17 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 16837 2021-02-03 10:22 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 12934 2020-09-16 10:17 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 12877 2021-06-22 11:24 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 55006 2021-07-07 17:18 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 3989 2020-07-17 12:01 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 11485 2020-05-14 09:28 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root 3760 2020-11-30 16:43 ./usr/include/htslib/hts_expr.h
-rw-r--r-- root/root 3944 2019-10-01 23:06 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root 2533 2021-02-03 10:22 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root 5605 2020-01-23 10:28 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 22899 2020-09-16 10:17 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 4050 2020-08-10 09:46 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5135 2019-11-19 11:20 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 3362 2021-02-03 10:22 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 3295 2020-08-27 11:09 ./usr/include/htslib/kroundup.h
-rw-r--r-- root/root 8916 2021-05-05 17:01 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 11480 2019-11-19 11:20 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 11090 2020-09-29 19:51 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 8881 2020-07-29 14:09 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 79223 2021-06-22 11:24 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 15920 2021-04-20 09:42 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 4942 2020-07-29 14:09 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 12747 2020-09-16 10:17 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root 62511 2021-02-10 11:27 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1686 2020-07-11 12:34 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4919 2020-09-16 10:17 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 4734660 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.13+ds
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 650 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 2680 2021-04-12 10:37 ./usr/share/doc/libhts-dev/README
-rw-r--r-- root/root 2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz
-rw-r--r-- root/root 401 2021-08-27 20:02 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root 5871 2021-08-27 20:02 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 24123 2021-07-07 17:18 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5897 2021-08-27 20:02 ./usr/share/doc/libhts-dev/copyright
libhts3-dbgsym_1.13+ds-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 1107944 bytes: control archive=824 bytes.
555 bytes, 13 lines control
617 bytes, 6 lines md5sums
Package: libhts3-dbgsym
Source: htslib
Version: 1.13+ds-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1218
Depends: libhts3 (= 1.13+ds-2)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libhts3
Build-Ids: 132f581baa26046f646906ccecff608c1166c130 3482194cefb6e802a813e62492f90a12883ccc27 4c2fc8973a74a94540171f6efd03eed75fc41c0f 864fe6f7503e872b26b4a4a6ede803703a2fa6b9 e8eca28d22b101bc64f7777a6f9c77ace8d3a6db
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/
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-rw-r--r-- root/root 14048 2021-08-27 20:02 ./usr/lib/debug/.build-id/13/2f581baa26046f646906ccecff608c1166c130.debug
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-rw-r--r-- root/root 45752 2021-08-27 20:02 ./usr/lib/debug/.build-id/34/82194cefb6e802a813e62492f90a12883ccc27.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/4c/
-rw-r--r-- root/root 23500 2021-08-27 20:02 ./usr/lib/debug/.build-id/4c/2fc8973a74a94540171f6efd03eed75fc41c0f.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/86/
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drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/e8/
-rw-r--r-- root/root 37996 2021-08-27 20:02 ./usr/lib/debug/.build-id/e8/eca28d22b101bc64f7777a6f9c77ace8d3a6db.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 11380 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/share/doc/libhts3-dbgsym -> libhts3
libhts3_1.13+ds-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 339224 bytes: control archive=4000 bytes.
1249 bytes, 23 lines control
890 bytes, 12 lines md5sums
30 bytes, 1 lines shlibs
14553 bytes, 544 lines symbols
67 bytes, 2 lines triggers
Package: libhts3
Source: htslib
Version: 1.13+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 830
Depends: libbz2-1.0, libc6 (>= 2.29), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.1.1), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.1.4)
Breaks: ivar (<< 1.3.1~), libhts-dev (<< 1.13~), libtabixpp (<< 1.0.0-5~), python3-pysam (<< 0.15~), samtools (<< 1.13~)
Replaces: libhts-dev (<< 1.13~)
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 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/
-rw-r--r-- root/root 9660 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
-rw-r--r-- root/root 26044 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
-rw-r--r-- root/root 26044 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
-rw-r--r-- root/root 13756 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
-rw-r--r-- root/root 693676 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.13+ds
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/lib/arm-linux-gnueabihf/libhts.so.3 -> libhts.so.1.13+ds
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
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-rw-r--r-- root/root 5871 2021-08-27 20:02 ./usr/share/doc/libhts3/changelog.Debian.gz
-rw-r--r-- root/root 24123 2021-07-07 17:18 ./usr/share/doc/libhts3/changelog.gz
-rw-r--r-- root/root 5897 2021-08-27 20:02 ./usr/share/doc/libhts3/copyright
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/man/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/man/man5/
-rw-r--r-- root/root 2452 2021-08-27 20:02 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root 1537 2021-08-27 20:02 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1857 2021-08-27 20:02 ./usr/share/man/man5/vcf.5.gz
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/man/man7/
-rw-r--r-- root/root 2167 2021-08-27 20:02 ./usr/share/man/man7/htslib-s3-plugin.7.gz
tabix-dbgsym_1.13+ds-2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 1419160 bytes: control archive=700 bytes.
450 bytes, 12 lines control
403 bytes, 4 lines md5sums
Package: tabix-dbgsym
Source: htslib
Version: 1.13+ds-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1585
Depends: tabix (= 1.13+ds-2)
Section: debug
Priority: optional
Description: debug symbols for tabix
Build-Ids: 5cea47cfb2b0c91b0cf0b48087fffe680d959ee7 cc4cb3173e95cc96666a8fce3142cf71aaa9fa62 d1a58f859fa4ae8fb786365e2a9179e59eb432af
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/5c/
-rw-r--r-- root/root 685444 2021-08-27 20:02 ./usr/lib/debug/.build-id/5c/ea47cfb2b0c91b0cf0b48087fffe680d959ee7.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/cc/
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drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.build-id/d1/
-rw-r--r-- root/root 687232 2021-08-27 20:02 ./usr/lib/debug/.build-id/d1/a58f859fa4ae8fb786365e2a9179e59eb432af.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 114688 2021-08-27 20:02 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-27 20:02 ./usr/share/doc/tabix-dbgsym -> tabix
tabix_1.13+ds-2_armhf.deb
-------------------------
new Debian package, version 2.0.
size 292468 bytes: control archive=1124 bytes.
981 bytes, 20 lines control
545 bytes, 9 lines md5sums
Package: tabix
Source: htslib
Version: 1.13+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 992
Depends: libbz2-1.0, libc6 (>= 2.7), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://github.com/samtools/htslib
Description: generic indexer for TAB-delimited genome position files
Tabix indexes files where some columns indicate sequence coordinates: name
(usually a chromosome), start and stop. The input data file must be position
sorted and compressed by bgzip (provided in this package), which has a gzip
like interface. After indexing, tabix is able to quickly retrieve data lines by
chromosomal coordinates. Fast data retrieval also works over network if an URI
is given as a file name.
.
This package is built from the HTSlib source, and provides the bgzip, htsfile,
and tabix tools.
drwxr-xr-x root/root 0 2021-08-27 20:02 ./
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/bin/
-rwxr-xr-x root/root 63080 2021-08-27 20:02 ./usr/bin/bgzip
-rwxr-xr-x root/root 444000 2021-08-27 20:02 ./usr/bin/htsfile
-rwxr-xr-x root/root 452188 2021-08-27 20:02 ./usr/bin/tabix
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/doc/tabix/
-rw-r--r-- root/root 5871 2021-08-27 20:02 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root 24123 2021-07-07 17:18 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root 5897 2021-08-27 20:02 ./usr/share/doc/tabix/copyright
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drwxr-xr-x root/root 0 2021-08-27 20:02 ./usr/share/man/man1/
-rw-r--r-- root/root 2602 2021-08-27 20:02 ./usr/share/man/man1/bgzip.1.gz
-rw-r--r-- root/root 1915 2021-08-27 20:02 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root 3318 2021-08-27 20:02 ./usr/share/man/man1/tabix.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 59768
Build-Time: 2264
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 346
Job: htslib_1.13+ds-2
Machine Architecture: armhf
Package: htslib
Package-Time: 2664
Source-Version: 1.13+ds-2
Space: 59768
Status: successful
Version: 1.13+ds-2
--------------------------------------------------------------------------------
Finished at 2021-09-02T06:23:22Z
Build needed 00:44:24, 59768k disc space