* Team upload.
[ Steve Langasek ]
* Fix autopkgtest on different architectures
[ Andreas Tille ]
* Cleanup d/rules
* No "Provides: libpbbam" due to ABI incompatibility
[dgit import unpatched pbbam 0.19.0+dfsg-4]
--- /dev/null
--- /dev/null
++pbbam for Debian
++----------------
++
++* The swig bindings require a version of swig higher than 3.0.2 (currently in unstable).
++ Without this, python and R bindings cannot be built.
++
++
++
++ -- Afif Elghraoui <afif@ghraoui.name>, Sun, 6 Sep 2015 13:57:45 -0700
++
--- /dev/null
--- /dev/null
++* Manpages for pbbamtools programs
++
++* package python and R bindings
++
++* package API documentation
--- /dev/null
--- /dev/null
++pbbam (0.19.0+dfsg-4) unstable; urgency=medium
++
++ * Team upload.
++
++ [ Steve Langasek ]
++ * Fix autopkgtest on different architectures
++
++ [ Andreas Tille ]
++ * Cleanup d/rules
++ * No "Provides: libpbbam" due to ABI incompatibility
++
++ -- Andreas Tille <tille@debian.org> Wed, 06 Feb 2019 09:16:06 +0100
++
++pbbam (0.19.0+dfsg-3) unstable; urgency=medium
++
++ * Team upload.
++
++ [ Steve Langasek ]
++ * Fix build dir name for tests
++ Closes: #909071
++
++ -- Andreas Tille <tille@debian.org> Mon, 04 Feb 2019 11:50:20 +0100
++
++pbbam (0.19.0+dfsg-2) unstable; urgency=medium
++
++ * Team upload.
++
++ [ Steve Langasek ]
++ * Provide generated files to autopkgtest
++ Closes: #921122
++
++ [ Andreas Tille ]
++ * debhelper 12
++ * Standards-Version: 4.3.0
++ * Secure URI in copyright format
++ * Remove trailing whitespace in debian/copyright
++
++ -- Andreas Tille <tille@debian.org> Sun, 03 Feb 2019 08:00:29 +0100
++
++pbbam (0.19.0+dfsg-1) unstable; urgency=medium
++
++ * Team upload.
++ * New upstream version
++ * Fix samtools call in tests
++ * d/control: Bump (fake) SOVERSION (=release version)
++
++ -- Andreas Tille <tille@debian.org> Wed, 10 Oct 2018 12:45:02 +0200
++
++pbbam (0.18.0+dfsg-2) unstable; urgency=medium
++
++ * Team upload.
++ * Missing Breaks+Replaces: libpbbam (<< 0.18)
++ Closes: #910206
++ * No needs-recommends restrictions, just Test-Depends: samtools
++
++ -- Andreas Tille <tille@debian.org> Wed, 03 Oct 2018 22:24:56 +0200
++
++pbbam (0.18.0+dfsg-1) unstable; urgency=medium
++
++ [ Andreas Tille ]
++ * Team upload.
++ * New upstream version
++ * Upstream is now tagging releases -> adapt watch file
++ * Upstream switched from cmake to meson
++ * debhelper 11
++ * Point Vcs fields to salsa.debian.org
++ * Standards-Version: 4.2.1
++ * Use d-shlibs
++ * Remove unneeded trigger
++ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test
++ * hardening=+all
++ * Add Breaks/Provides/Replaces libpbbam
++
++ [ Fabian Kloetzl ]
++ * fix dependency check for meson
++
++ -- Andreas Tille <tille@debian.org> Thu, 06 Sep 2018 14:29:53 +0200
++
++pbbam (0.7.4+ds-1) unstable; urgency=medium
++
++ * New upstream release snapshot
++ - Exclude dependency convenience copy
++ - Update patches
++ - Update running of tests at build-time
++ - Update .install files
++ - Update autopkgtest commands
++ * Use debhelper compat 10
++ * libpbbam-dev: depend on libssl-dev
++
++ -- Afif Elghraoui <afif@debian.org> Sat, 21 Jan 2017 23:48:21 -0800
++
++pbbam (0.7.0-1) unstable; urgency=medium
++
++ * Imported Upstream version 0.7.0
++ * Update patches
++
++ -- Afif Elghraoui <afif@debian.org> Sun, 30 Oct 2016 14:31:49 -0700
++
++pbbam (0.5.0-3) unstable; urgency=low
++
++ * Fix cmake arguments to properly position LDFLAGS for -Wl,--as-needed.
++ Thanks to Steve Langasek (Closes: #841671)
++
++ -- Afif Elghraoui <afif@debian.org> Sun, 23 Oct 2016 14:07:27 -0700
++
++pbbam (0.5.0-2) unstable; urgency=low
++
++ * libpbbam-dev: add dependency on libhts-dev
++
++ -- Afif Elghraoui <afif@debian.org> Sun, 17 Jul 2016 23:29:34 -0700
++
++pbbam (0.5.0-1) unstable; urgency=medium
++
++ * New upstream revision (git 79ab246 from 2016-02-23)
++ * Declare additional copyrights to avoid repacking tarball
++ * Update patches
++ * Update Standards-Version to 3.9.8
++ * Use encrypted protocols for VCS URLs
++ * Clean up d/control and d/rules
++ * Use dh-exec for library installation rather than sed-within-d/rules
++ * Set up build-time tests for command-line tools
++ * Add binary package for command-line tools
++ * Install library to main library path
++ * Configure autopkgtests
++ * Use documentation page as Homepage
++ * Remove build-dependency on doxygen
++ * Add TODO list
++
++ -- Afif Elghraoui <afif@debian.org> Tue, 05 Jul 2016 03:25:49 -0700
++
++pbbam (0.1.0~20150813+git4e9e417+dfsg-1) unstable; urgency=low
++
++ * Initial release (Closes: #798220)
++
++ -- Afif Elghraoui <afif@ghraoui.name> Fri, 18 Sep 2015 02:40:24 -0700
--- /dev/null
--- /dev/null
++12
--- /dev/null
--- /dev/null
++Source: pbbam
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders: Afif Elghraoui <afif@debian.org>
++Section: science
++Priority: optional
++Build-Depends: debhelper (>= 12~),
++ dh-exec,
++ d-shlibs,
++ meson,
++ pkg-config,
++ python,
++# swig3.0,
++ libboost-dev (>= 1.54),
++ zlib1g-dev,
++ libssl-dev,
++ libhts-dev,
++# Test-Depends:
++ libgtest-dev,
++ python-cram,
++ samtools
++Standards-Version: 4.3.0
++Vcs-Browser: https://salsa.debian.org/med-team/pbbam
++Vcs-Git: https://salsa.debian.org/med-team/pbbam.git
++Homepage: http://pbbam.readthedocs.org/en/latest/index.html
++
++Package: pbbamtools
++Architecture: any
++Depends: ${shlibs:Depends},
++ ${misc:Depends},
++ libpbbam0.19.0 (= ${binary:Version})
++Recommends: samtools
++Description: processing Pacific Biosciences binary alignment/map files
++ The BAM format is a binary, compressed, record-oriented container format
++ for raw or aligned sequence reads. The associated SAM format is a text
++ representation of the same data. The specifications for BAM/SAM are maintained
++ by the SAM/BAM Format Specification Working Group.
++ .
++ PacBio-produced BAM files are fully compatible with the BAM specification,
++ but makes use of the extensibility mechanisms of the BAM specification to
++ encode PacBio-specific information.
++ .
++ This package provides command-line utilities for working with PacBio BAM
++ files.
++
++Package: libpbbam0.19.0
++Architecture: any
++Multi-Arch: same
++Section: libs
++Depends: ${shlibs:Depends},
++ ${misc:Depends}
++Pre-Depends: ${misc:Pre-Depends}
++Breaks: libpbbam (<< ${source:Version})
++Replaces: libpbbam
++Description: Pacific Biosciences binary alignment/map (BAM) library
++ The BAM format is a binary, compressed, record-oriented container format
++ for raw or aligned sequence reads. The associated SAM format is a text
++ representation of the same data. The specifications for BAM/SAM are maintained
++ by the SAM/BAM Format Specification Working Group.
++ .
++ PacBio-produced BAM files are fully compatible with the BAM specification,
++ but makes use of the extensibility mechanisms of the BAM specification to
++ encode PacBio-specific information. The pbbam library provides tools to
++ work with these files
++
++Package: libpbbam-dev
++Architecture: any
++Section: libdevel
++Depends: libpbbam0.19.0 (= ${binary:Version}),
++ libhts-dev,
++ libssl-dev,
++ ${misc:Depends}
++Breaks: libpbbam (<< 0.18)
++Replaces: libpbbam (<< 0.18)
++Description: Pacific Biosciences binary alignment/map (BAM) library (headers)
++ The BAM format is a binary, compressed, record-oriented container format
++ for raw or aligned sequence reads. The associated SAM format is a text
++ representation of the same data. The specifications for BAM/SAM are maintained
++ by the SAM/BAM Format Specification Working Group.
++ .
++ PacBio-produced BAM files are fully compatible with the BAM specification,
++ but makes use of the extensibility mechanisms of the BAM specification to
++ encode PacBio-specific information. The pbbam library provides tools to
++ work with these files
++ .
++ This package contains the library header files.
--- /dev/null
--- /dev/null
++Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
++Upstream-Name: pbbam
++Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
++Source: https://github.com/PacificBiosciences/pbbam
++Files-Excluded: third-party
++ */clang-format*
++
++Files: *
++Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>
++License: PacBio-BSD-3-Clause
++
++Files: src/pugixml/*
++Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine@gmail.com>
++ 2003 Kristen Wegner <kristen@tima.net>
++License: MIT
++
++Files: tools/common/OptionParser.*
++Copyright: 2010 Johannes Weißl <jargon@molb.org>
++License: BSD-3-Clause or BSD-2-Clause
++
++Files: debian/*
++Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
++License: PacBio-BSD-3-Clause
++
++License: PacBio-BSD-3-Clause
++ Redistribution and use in source and binary forms, with or without
++ modification, are permitted (subject to the limitations in the
++ disclaimer below) provided that the following conditions are met:
++ 1. Redistributions of source code must retain the above copyright
++ notice, this list of conditions and the following disclaimer.
++ 2. Redistributions in binary form must reproduce the above
++ copyright notice, this list of conditions and the following
++ disclaimer in the documentation and/or other materials provided
++ with the distribution.
++ 3. Neither the name of Pacific Biosciences nor the names of its
++ contributors may be used to endorse or promote products derived
++ from this software without specific prior written permission.
++ .
++ NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
++ GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
++ BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
++ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
++ OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
++ DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
++ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
++ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
++ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
++ USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
++ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
++ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
++ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
++ SUCH DAMAGE.
++
++License: BSD-3-Clause
++ Redistribution and use in source and binary forms, with or without
++ modification, are permitted provided that the following conditions
++ are met:
++ 1. Redistributions of source code must retain the above copyright
++ notice, this list of conditions and the following disclaimer.
++ 2. Redistributions in binary form must reproduce the above copyright
++ notice, this list of conditions and the following disclaimer in the
++ documentation and/or other materials provided with the distribution.
++ 3. Neither the name of the University nor the names of its contributors
++ may be used to endorse or promote products derived from this software
++ without specific prior written permission.
++ .
++ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
++ ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
++ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
++ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE HOLDERS OR
++ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
++ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
++ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
++ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
++ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
++ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
++ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
++
++License: BSD-2-Clause
++ Redistribution and use in source and binary forms, with or without
++ modification, are permitted provided that the following conditions
++ are met:
++ 1. Redistributions of source code must retain the above copyright
++ notice, this list of conditions and the following disclaimer.
++ 2. Redistributions in binary form must reproduce the above
++ copyright notice, this list of conditions and the following
++ disclaimer in the documentation and/or other materials provided
++ with the distribution.
++ .
++ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
++ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
++ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
++ FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
++ COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
++ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
++ BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
++ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
++ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
++ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
++ WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
++ POSSIBILITY OF SUCH DAMAGE.
++
++License: MIT
++ Permission is hereby granted, free of charge, to any person
++ obtaining a copy of this software and associated documentation
++ files (the "Software"), to deal in the Software without
++ restriction, including without limitation the rights to use,
++ copy, modify, merge, publish, distribute, sublicense, and/or sell
++ copies of the Software, and to permit persons to whom the
++ Software is furnished to do so, subject to the following
++ conditions:
++ .
++ The above copyright notice and this permission notice shall be
++ included in all copies or substantial portions of the Software.
++ .
++ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
++ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
++ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
++ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
++ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
++ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
++ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
++ OTHER DEALINGS IN THE SOFTWARE.
--- /dev/null
--- /dev/null
++Description: Only debug code to track down bug #909071 i386 (no solution yet)
++Bug-Debian: https://bugs.debian.org/909071
++Author: Andreas Tille <tille@debian.org>
++Last-Update: Tue, 18 Sep 2018 08:40:19 +0200
++
++--- a/tests/src/cram/pbmerge_pacbio_ordering.t.in
+++++ b/tests/src/cram/pbmerge_pacbio_ordering.t.in
++@@ -13,6 +13,8 @@ Setup:
++
++ Sanity Check:
++
+++ $ ls -l $HQREGION_BAM
+++ $ echo "DEBUG: $BAM2SAM --header-only $HQREGION_BAM"
++ $ $BAM2SAM --header-only $HQREGION_BAM
++ @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
++ @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
++@@ -20,9 +22,11 @@ Sanity Check:
++ @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc)
++ @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc)
++
+++ $ echo "DEBUG: $BAM2SAM --no-header $HQREGION_BAM | cut -f 1"
++ $ $BAM2SAM --no-header $HQREGION_BAM | cut -f 1
++ ArminsFakeMovie/100000/2659_7034
++
+++ $ $echo "DEBUG: BAM2SAM --header-only $SCRAPS_BAM"
++ $ $BAM2SAM --header-only $SCRAPS_BAM
++ @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
++ @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
++@@ -30,6 +34,7 @@ Sanity Check:
++ @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc)
++ @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc)
++
+++ $ echo "DEBUG: $BAM2SAM --no-header $SCRAPS_BAM | cut -f 1"
++ $ $BAM2SAM --no-header $SCRAPS_BAM | cut -f 1
++ ArminsFakeMovie/100000/0_2659
++ ArminsFakeMovie/100000/3025_3047
++--- a/tests/src/cram/pbmerge_aligned_ordering.t.in
+++++ b/tests/src/cram/pbmerge_aligned_ordering.t.in
++@@ -51,7 +51,10 @@ Sanity Check:
++
++ Normal Merge:
++
+++ $ echo "DEBUG: $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM"
++ $ $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM
+++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 1: File $MERGED_BAM does not exists - no idea why. Try again creating it after 5s."; $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ; fi
+++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 1: File $MERGED_BAM does not exists - even after trying again."; exit ; else echo echo "File $MERGED_BAM was created now" ; fi
++
++ $ $BAM2SAM --header-only $MERGED_BAM
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++@@ -60,6 +63,7 @@ Normal Merge:
++ @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
++ @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
++
+++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
++ $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
++@@ -86,8 +90,15 @@ Normal Merge:
++
++ Shuffle Input:
++
+++ $ echo DEBUG: PATH = $PATH
+++ $ which pbmerge
+++ $ echo "DEBUG: $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM"
++ $ $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM
+++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 2: File $MERGED_BAM does not exists - no idea why. Try again creating it after 5s."; $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ; fi
+++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 2: File $MERGED_BAM does not exists - even after trying again."; exit ; else echo echo "File $MERGED_BAM was created now" ; fi
++
+++ $ echo "DEBUG: $BAM2SAM --header-only $MERGED_BAM"
+++ $ echo "DEBUG: That is the problematic command"
++ $ $BAM2SAM --header-only $MERGED_BAM
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++@@ -95,6 +106,7 @@ Shuffle Input:
++ @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
++ @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
++
+++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
++ $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
++@@ -130,6 +142,7 @@ Explicit Output Filename (also enables P
++ @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
++ @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
++
+++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
++ $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
++@@ -169,6 +182,7 @@ Explicit Output Filename (with disabled
++ @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
++ @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc)
++
+++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20"
++ $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
--- /dev/null
--- /dev/null
++Author: Andreas Tille, Fabian Klötzl
++Last-Update: 2018-09-05 14:50:07 +0000
++Description: Use Debian packaged gtest
++
++--- a/tests/meson.build
+++++ b/tests/meson.build
++@@ -6,7 +6,7 @@ if not pbbam_cram_script.found()
++ pbbam_cram_script = find_program('scripts/cram.py', required : true)
++ endif
++
++-pbbam_gtest_dep = dependency('gtest_main', fallback : ['gtest', 'gtest_main_dep'])
+++pbbam_gtest_dep = dependency('gtest', main: true)
++
++ pbbam_PbbamTestData_h_config = configuration_data()
++ pbbam_PbbamTestData_h_config.set('PacBioBAM_BinDir', join_paths([meson.current_build_dir(), '../tools']))
--- /dev/null
--- /dev/null
++fix_gtest_depcheck.patch
++# debug_tests.patch
--- /dev/null
--- /dev/null
++*/bin /usr
--- /dev/null
--- /dev/null
++#!/usr/bin/make -f
++
++#DH_VERBOSE = 1
++export LC_ALL=C.UTF-8
++include /usr/share/dpkg/default.mk
++
++export DEB_BUILD_MAINT_OPTIONS=hardening=+all
++
++DEB_VERSION_UPSTREAM := $(subst +ds,,$(DEB_VERSION_UPSTREAM))
++generated_data_dir = $(CURDIR)/gendata
++
++%:
++ dh $@ --buildsystem=meson
++
++override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))
++ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
++ dh_auto_configure -O--buildsystem=meson
++ mkdir -p $(generated_data_dir)
++ python tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir)
++ # Fix broken PATH
++ synthetic_movie_all_path=`find $$PWD -name synthetic_movie_all.subreadset.xml` ; \
++ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?$${synthetic_movie_all_path}?" tests/src/cram/pbbamify*
++ BINDIR=`dirname $$(find $$PWD -name pbmerge -type f -executable)`; \
++ LIBDIR=`find $$PWD -name lib -type d`; \
++ PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \
++ cram -v --preserve-env $^
++endif
++
++override_dh_installchangelogs:
++ dh_installchangelogs CHANGELOG.md
++
++override_dh_auto_clean:
++ dh_auto_clean
++ find -name "*.deb.t" -delete
++ $(RM) -r $(generated_data_dir)
++
++%.deb.t: %.t.in
++ sed \
++ -e 's/$$BAM2SAM/samtools view/g' \
++ -e 's/\-\-header\-only/-H/g' \
++ -e 's/\-\-no\-header//g' \
++ -e 's|@PacBioBAM_BinDir@/||g' \
++ -e 's|$$TOOLS_BIN/||g' \
++ -e 's|@PacBioBAM_TestsDir@|$(CURDIR)/tests|g' \
++ -e 's|@PacBioBAM_VERSION@|$(DEB_VERSION_UPSTREAM)|g' \
++ -e 's|@GeneratedTestDataDir@|$(generated_data_dir)|g' \
++ -e '/@PG/s|+dfsg||g' \
++ -e 's/$$SAMTOOLS/samtools/g' \
++ $< > $@
++
++override_dh_install:
++ dh_install
++ d-shlibmove --commit \
++ --multiarch \
++ --devunversioned \
++ --exclude-la \
++ --exclude-a \
++ --override s/libhts2-dev/libhts-dev/ \
++ --movedev debian/tmp/usr/include/* usr/include \
++ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
++ debian/tmp/usr/lib/*/*.so
--- /dev/null
--- /dev/null
++3.0 (quilt)
--- /dev/null
--- /dev/null
++Test-Command: debian/rules override_dh_auto_test
++Depends:
++ @builddeps@,
++ pbbamtools,
++Restrictions: rw-build-tree, allow-stderr
--- /dev/null
--- /dev/null
++version=4
++
++opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
++ https://github.com/PacificBiosciences/pbbam/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
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