--- /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
+* Manpages for pbbamtools programs
+
+* package python and R bindings
+
+* package API documentation
--- /dev/null
+pbbam (0.23.0+dfsg-1) unstable; urgency=medium
+
+ * Afif removed himself from Uploaders
+ * Add myself to Uploaders
+ * New upstream version
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Set upstream metadata fields: Contact, Name.
+ * Rename library to libpbbam0.23.0 due to upstream choice of ABI version
+ * Remove code copy of python-cram from upstream source
+ * Build-Depends: python3-cram
+ * d/control: Use <!nocheck> instead of comment
+
+ -- Andreas Tille <tille@debian.org> Sun, 04 Aug 2019 21:16:32 +0200
+
+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-3.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Apply autopkgtest regression fix from Steve Langasek.
+ (Closes: #908269)
+ * libpbbam0.19.0: Remove the incorrect Provides: libpbbam.
+
+ -- Adrian Bunk <bunk@debian.org> Wed, 06 Feb 2019 08:53:24 +0200
+
+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
+Source: pbbam
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 12),
+ dh-exec,
+ d-shlibs,
+ meson,
+ pkg-config,
+# swig3.0,
+ libboost-dev,
+ zlib1g-dev,
+ libssl-dev,
+ libhts-dev,
+ libgtest-dev <!nocheck>,
+ python3-cram <!nocheck>,
+ samtools <!nocheck>
+Standards-Version: 4.4.0
+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},
+ libpbbam0.23.0 (= ${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: libpbbam0.23.0
+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: libpbbam0.23.0 (= ${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
+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*
+ */tests/scripts/cram*
+
+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
+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
+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
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 04 Aug 2019 09:15:35 +0200
+Description: Use Python3 in build time test suite
+
+--- a/meson.build
++++ b/meson.build
+@@ -80,7 +80,7 @@ subdir('src')
+
+ if not meson.is_subproject()
+ if get_option('build-tools') or get_option('tests')
+- pbbam_python = find_program('python')
++ pbbam_python = find_program('python3')
+
+ if get_option('tests')
+ pbbam_clang_formatter = find_program('tools/check-formatting')
+--- a/tests/scripts/generate_data.py
++++ b/tests/scripts/generate_data.py
+@@ -1,7 +1,4 @@
+-#!/usr/bin/env python
+-
+-from __future__ import print_function
+-from __future__ import unicode_literals
++#!/usr/bin/python3
+
+ import os, shutil, sys
+ from io import StringIO
+@@ -177,9 +174,9 @@ class TestDataGenerator:
+ # else silent success
+ if self.outputFiles or self.outputSymlinks:
+ print('Generating test data in %s ' % self.generatedDataDir)
+- for file, func in self.outputFiles.items():
++ for file, func in list(self.outputFiles.items()):
+ func(file)
+- for link, func in self.outputSymlinks.items():
++ for link, func in list(self.outputSymlinks.items()):
+ func(link)
+
+ # script entry point
--- /dev/null
+fix_gtest_depcheck.patch
+# debug_tests.patch
+use_debian_packaged_python3-cram.patch
+python3.patch
--- /dev/null
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 04 Aug 2019 09:15:35 +0200
+Description: Use python3-cram instead of cram code copy
+
+--- a/tests/meson.build
++++ b/tests/meson.build
+@@ -1,6 +1,6 @@
+ subdir('src')
+
+-pbbam_cram_script = find_program('cram', required : false)
++pbbam_cram_script = find_program('cram3', required : false)
+ if not pbbam_cram_script.found()
+ warning('Using bundled cram script')
+ pbbam_cram_script = find_program('scripts/cram.py', required : true)
--- /dev/null
+*/bin /usr
--- /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)
+ python3 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="$$LIBDIR:$(LD_LIBRARY_PATH)" \
+ cram3 -v --preserve-env $^
+endif
+
+override_dh_installchangelogs:
+ dh_installchangelogs CHANGELOG.md
+
+override_dh_auto_clean:
+ dh_auto_clean
+ find -name "*.deb.t" -delete
+ $(RM) -r $(generated_data_dir)
+
+%.deb.t: %.t.in
+ sed \
+ -e 's/$$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
+3.0 (quilt)
--- /dev/null
+Test-Command: debian/rules override_dh_auto_test
+Depends:
+ @builddeps@,
+ pbbamtools,
+Restrictions: rw-build-tree, allow-stderr
--- /dev/null
+Name: pbbam
+Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
--- /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@
projects / pbbam.git / commitdiff