--- /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 (1.0.6+dfsg-2) unstable; urgency=medium
++
++ * Reupload to enable testing migration
++
++ -- Andreas Tille <tille@debian.org> Sat, 21 Dec 2019 13:30:52 +0100
++
++pbbam (1.0.6+dfsg-1) unstable; urgency=medium
++
++ * Drop <!nocheck> option from python3-cram
++ Closes: #934467
++ * New upstream version
++ * Standards-Version: 4.4.1
++ * Remove patch debug_tests.patch that is missing from
++ debian/patches/series.
++ * debian/copyright: use spaces rather than tabs to start continuation
++ lines.
++ * Remove obsolete fields Contact, Name from debian/upstream/metadata.
++ * Build-Depends: cmake, libpbcopper-dev (>= 1.3.0)
++ * Adapt test results to latest samtools
++ * d-shlibs override for libpbcopper1.3.0-dev
++ * Unfortunately upstream does not distinguish between release version
++ and SOVERSION - just follow their versioning anyway and rename
++ dynamic library package
++
++ -- Andreas Tille <tille@debian.org> Fri, 20 Dec 2019 11:27:03 +0100
++
++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
--- /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,
++ cmake,
++# swig3.0,
++ libboost-dev,
++ zlib1g-dev,
++ libssl-dev,
++ libhts-dev,
++ libpbcopper-dev (>= 1.3.0),
++ python3-cram,
++ libgtest-dev <!nocheck>,
++ samtools <!nocheck>
++Standards-Version: 4.4.1
++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},
++ libpbbam1.0.6 (= ${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: libpbbam1.0.6
++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: libpbbam1.0.6 (= ${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*
++ */tests/scripts/cram*
++
++Files: *
++Copyright: 2014-2019 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: debian/*
++Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
++ 2016-2019 Andreas Tille <tille@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: 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
++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
++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
++@@ -83,7 +83,7 @@ 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
--- /dev/null
++Description: Adapt test results to latest samtools
++Author: Andreas Tille <tille@debian.org>
++Last-Update: Fri, 13 Dec 2019 21:50:03 +0100
++
++--- a/tests/src/cram/pbmerge_pacbio_ordering.t.in
+++++ b/tests/src/cram/pbmerge_pacbio_ordering.t.in
++@@ -13,7 +13,7 @@ Setup:
++
++ Sanity Check:
++
++- $ $BAM2SAM --header-only $HQREGION_BAM
+++ $ $BAM2SAM --header-only $HQREGION_BAM | grep -v 'CL:samtools view -H '
++ @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)
++ @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc)
++@@ -23,7 +23,7 @@ Sanity Check:
++ $ $BAM2SAM --no-header $HQREGION_BAM | cut -f 1
++ ArminsFakeMovie/100000/2659_7034
++
++- $ $BAM2SAM --header-only $SCRAPS_BAM
+++ $ $BAM2SAM --header-only $SCRAPS_BAM | grep -v 'CL:samtools view -H '
++ @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)
++ @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc)
++@@ -105,7 +105,7 @@ Normal Merge:
++
++ $ $PBMERGE $HQREGION_BAM $SCRAPS_BAM > $MERGED_BAM
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @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\tPM:SEQUEL (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\tPM:SEQUEL (esc)
++@@ -192,7 +192,7 @@ Shuffle Input:
++
++ $ $PBMERGE $SCRAPS_BAM $HQREGION_BAM > $MERGED_BAM
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @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\tPM:SEQUEL (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\tPM:SEQUEL (esc)
++@@ -279,7 +279,7 @@ Explicit Output Filename (also enables P
++
++ $ $PBMERGE -o $MERGED_BAM $HQREGION_BAM $SCRAPS_BAM
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @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\tPM:SEQUEL (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\tPM:SEQUEL (esc)
++@@ -370,7 +370,7 @@ Explicit Output Filename (with disabled
++
++ $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @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\tPM:SEQUEL (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\tPM:SEQUEL (esc)
++--- a/tests/src/cram/pbmerge_mixed_ordering.t.in
+++++ b/tests/src/cram/pbmerge_mixed_ordering.t.in
++@@ -12,7 +12,7 @@ Setup:
++
++ Sanity Check:
++
++- $ $BAM2SAM --header-only $UNALIGNED_BAM
+++ $ $BAM2SAM --header-only $UNALIGNED_BAM | grep -v 'CL:samtools view -H '
++ @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)
++ @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc)
++@@ -22,7 +22,7 @@ Sanity Check:
++ $ $BAM2SAM --no-header $UNALIGNED_BAM | cut -f 1
++ ArminsFakeMovie/100000/2659_7034
++
++- $ $BAM2SAM --header-only $ALIGNED_BAM
+++ $ $BAM2SAM --header-only $ALIGNED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377 (esc)
++--- a/tests/src/cram/pbmerge_aligned_ordering.t.in
+++++ b/tests/src/cram/pbmerge_aligned_ordering.t.in
++@@ -13,7 +13,7 @@ Setup:
++
++ Sanity Check:
++
++- $ $BAM2SAM --header-only $INPUT_1
+++ $ $BAM2SAM --header-only $INPUT_1 | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377 (esc)
++@@ -31,7 +31,7 @@ Sanity Check:
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
++ m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
++
++- $ $BAM2SAM --header-only $INPUT_2
+++ $ $BAM2SAM --header-only $INPUT_2 | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377 (esc)
++@@ -53,7 +53,7 @@ Normal Merge:
++
++ $ $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
++@@ -88,7 +88,7 @@ Shuffle Input:
++
++ $ $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
++@@ -123,7 +123,7 @@ Explicit Output Filename (also enables P
++
++ $ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
++@@ -162,7 +162,7 @@ Explicit Output Filename (with disabled
++
++ $ $PBMERGE -o $MERGED_BAM --no-pbi $INPUT_1 $INPUT_2
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
++--- a/tests/src/cram/pbbamify.t.in
+++++ b/tests/src/cram/pbbamify.t.in
++@@ -8,7 +8,7 @@ Setup:
++
++ Forward alignments with and without user specified tags, one alignment with undefined mapq, some alignments with basic CIGAR operations, 2 alignemtns with hard clipping, and several invalid alignments (1 without a seq field and 1 not present in the dataset) which should be skipped:
++
++- $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h
+++ $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
++ @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
++ @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
++ @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc)
++@@ -36,7 +36,7 @@ Forward alignments with and without user
++ $ rm pbbamify.log
++
++ Reverse alignments: 2 primary alignments and 7 secondary, 6 alignments with extended CIGAR and 2 with basic CIGAR strings, 1 alignment with undefined (255) mapq, 2 alignments with hard clipping, 1 alignment with user defined tag. All alignments have a read group assigned which is different than the dataset.
++- $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | $SAMTOOLS view -h
+++ $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
++ @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
++ @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
++ @RG\tID:7a515ee0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_2\tPM:SEQUEL (esc)
++@@ -60,7 +60,7 @@ Reverse alignments: 2 primary alignments
++
++ CCS read:
++
++- $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | $SAMTOOLS view -h
+++ $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
++ @HD\tVN:1.5\tSO:unknown\tpb:3.0.1 (esc)
++ @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
++ @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc)
++@@ -74,7 +74,7 @@ CCS read:
++
++ No verbose output:
++
++- $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h
+++ $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
++ @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
++ @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
++ @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc)
++@@ -101,7 +101,7 @@ No verbose output:
++
++ Test on a dataset, input contains alignments from all subread sets.
++
++- $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa $GENERATEDDATADIR/synthetic_movie_all.subreadset.xml | $SAMTOOLS view -h
+++ $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa $GENERATEDDATADIR/synthetic_movie_all.subreadset.xml | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
++ @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
++ @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
++ @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc)
++--- a/tests/src/cram/pbmerge_fofn.t.in
+++++ b/tests/src/cram/pbmerge_fofn.t.in
++@@ -14,7 +14,7 @@ Setup:
++
++ Sanity Check:
++
++- $ $BAM2SAM --header-only $INPUT_1
+++ $ $BAM2SAM --header-only $INPUT_1 | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc)
++@@ -26,7 +26,7 @@ Sanity Check:
++ singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc)
++ singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc)
++
++- $ $BAM2SAM --header-only $INPUT_2
+++ $ $BAM2SAM --header-only $INPUT_2 | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:b89a4406\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;FRAMERATEHZ=100;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
++@@ -54,7 +54,7 @@ Normal Merge from FOFN:
++ $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
++ Found
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc)
++@@ -92,7 +92,7 @@ Normal Merge from FOFN (disabled PBI):
++ $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
++ Not found
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
++ @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
++ @RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc)
++--- a/tests/src/cram/pbmerge_dataset.t.in
+++++ b/tests/src/cram/pbmerge_dataset.t.in
++@@ -59,7 +59,7 @@ Normal Merge from XML:
++ $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
++ Found
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
++ @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
++ @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
++@@ -91,7 +91,7 @@ Normal Merge from XML (disabled PBI):
++ $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
++ Not found
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
++ @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
++ @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
++@@ -122,7 +122,7 @@ Write to stdout:
++ $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
++ Not found
++
++- $ $BAM2SAM --header-only $MERGED_BAM
+++ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
++ @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
++ @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
++ @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
--- /dev/null
--- /dev/null
++fix_gtest_depcheck.patch
++# debug_tests.patch
++use_debian_packaged_python3-cram.patch
++python3.patch
++results_with_latest_samtools.patch
--- /dev/null
--- /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
--- /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)
++ 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' \
++ $< > $@
++
++override_dh_install:
++ dh_install
++ d-shlibmove --commit \
++ --multiarch \
++ --devunversioned \
++ --exclude-la \
++ --exclude-a \
++ --override s/libhts2-dev/libhts-dev/ \
++ --override s/libpbcopper1.3.0-dev/libpbcopper-dev/ \
++ --movedev debian/tmp/usr/include/* usr/include \
++ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(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@
projects / pbbam.git / commitdiff