From: Andreas Tille Date: Sat, 21 Dec 2019 12:30:52 +0000 (+0000) Subject: Import pbbam_1.0.6+dfsg-2.debian.tar.xz X-Git-Tag: archive/raspbian/1.0.6+dfsg-2+rpi1^2~5^2 X-Git-Url: https://dgit.raspbian.org/%22http://www.example.com/cgi/%22/%22http:/www.example.com/cgi/%22?a=commitdiff_plain;h=17f416f57712515344855cd30beb2f8e071ed029;p=pbbam.git Import pbbam_1.0.6+dfsg-2.debian.tar.xz [dgit import tarball pbbam 1.0.6+dfsg-2 pbbam_1.0.6+dfsg-2.debian.tar.xz] --- 17f416f57712515344855cd30beb2f8e071ed029 diff --git a/README.source b/README.source new file mode 100644 index 0000000..c29c516 --- /dev/null +++ b/README.source @@ -0,0 +1,10 @@ +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 , Sun, 6 Sep 2015 13:57:45 -0700 + diff --git a/TODO b/TODO new file mode 100644 index 0000000..c86d636 --- /dev/null +++ b/TODO @@ -0,0 +1,5 @@ +* Manpages for pbbamtools programs + +* package python and R bindings + +* package API documentation diff --git a/changelog b/changelog new file mode 100644 index 0000000..21146a0 --- /dev/null +++ b/changelog @@ -0,0 +1,185 @@ +pbbam (1.0.6+dfsg-2) unstable; urgency=medium + + * Reupload to enable testing migration + + -- Andreas Tille Sat, 21 Dec 2019 13:30:52 +0100 + +pbbam (1.0.6+dfsg-1) unstable; urgency=medium + + * Drop 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 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 instead of comment + + -- Andreas Tille 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 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 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 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 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 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 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 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 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 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 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 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 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 Fri, 18 Sep 2015 02:40:24 -0700 diff --git a/control b/control new file mode 100644 index 0000000..7ac5683 --- /dev/null +++ b/control @@ -0,0 +1,85 @@ +Source: pbbam +Maintainer: Debian Med Packaging Team +Uploaders: Andreas Tille +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 , + samtools +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. diff --git a/copyright b/copyright new file mode 100644 index 0000000..db047eb --- /dev/null +++ b/copyright @@ -0,0 +1,72 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: pbbam +Upstream-Contact: Pacific Biosciences +Source: https://github.com/PacificBiosciences/pbbam +Files-Excluded: third-party + */clang-format* + */tests/scripts/cram* + +Files: * +Copyright: 2014-2019 Pacific Biosciences of California, Inc. +License: PacBio-BSD-3-Clause + +Files: src/pugixml/* +Copyright: 2006-2014 Arseny Kapoulkine + 2003 Kristen Wegner +License: MIT + +Files: debian/* +Copyright: 2015-2016 Afif Elghraoui + 2016-2019 Andreas Tille +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. diff --git a/patches/fix_gtest_depcheck.patch b/patches/fix_gtest_depcheck.patch new file mode 100644 index 0000000..490d279 --- /dev/null +++ b/patches/fix_gtest_depcheck.patch @@ -0,0 +1,15 @@ +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'])) diff --git a/patches/python3.patch b/patches/python3.patch new file mode 100644 index 0000000..b3795c5 --- /dev/null +++ b/patches/python3.patch @@ -0,0 +1,38 @@ +Author: Andreas Tille +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 diff --git a/patches/results_with_latest_samtools.patch b/patches/results_with_latest_samtools.patch new file mode 100644 index 0000000..8fa5af0 --- /dev/null +++ b/patches/results_with_latest_samtools.patch @@ -0,0 +1,250 @@ +Description: Adapt test results to latest samtools +Author: Andreas Tille +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) diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..92ca5bd --- /dev/null +++ b/patches/series @@ -0,0 +1,5 @@ +fix_gtest_depcheck.patch +# debug_tests.patch +use_debian_packaged_python3-cram.patch +python3.patch +results_with_latest_samtools.patch diff --git a/patches/use_debian_packaged_python3-cram.patch b/patches/use_debian_packaged_python3-cram.patch new file mode 100644 index 0000000..8a94cfc --- /dev/null +++ b/patches/use_debian_packaged_python3-cram.patch @@ -0,0 +1,14 @@ +Author: Andreas Tille +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) diff --git a/pbbamtools.install b/pbbamtools.install new file mode 100644 index 0000000..7380180 --- /dev/null +++ b/pbbamtools.install @@ -0,0 +1 @@ +*/bin /usr diff --git a/rules b/rules new file mode 100755 index 0000000..684cf69 --- /dev/null +++ b/rules @@ -0,0 +1,62 @@ +#!/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 diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..9b21e04 --- /dev/null +++ b/tests/control @@ -0,0 +1,5 @@ +Test-Command: debian/rules override_dh_auto_test +Depends: + @builddeps@, + pbbamtools, +Restrictions: rw-build-tree, allow-stderr diff --git a/watch b/watch new file mode 100644 index 0000000..1b64644 --- /dev/null +++ b/watch @@ -0,0 +1,4 @@ +version=4 + +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ + https://github.com/PacificBiosciences/pbbam/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@