From: Andreas Tille Date: Sat, 21 Dec 2019 12:30:52 +0000 (+0000) Subject: pbbam (1.0.6+dfsg-2) unstable; urgency=medium X-Git-Tag: archive/raspbian/1.0.6+dfsg-2+rpi1^2~5 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=aee7f58709b72a1c77036ec414ff5002e886a8e4;p=pbbam.git pbbam (1.0.6+dfsg-2) unstable; urgency=medium * Reupload to enable testing migration [dgit import unpatched pbbam 1.0.6+dfsg-2] --- aee7f58709b72a1c77036ec414ff5002e886a8e4 diff --cc debian/README.source index 0000000,0000000..c29c516 new file mode 100644 --- /dev/null +++ b/debian/README.source @@@ -1,0 -1,0 +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 --cc debian/TODO index 0000000,0000000..c86d636 new file mode 100644 --- /dev/null +++ b/debian/TODO @@@ -1,0 -1,0 +1,5 @@@ ++* Manpages for pbbamtools programs ++ ++* package python and R bindings ++ ++* package API documentation diff --cc debian/changelog index 0000000,0000000..21146a0 new file mode 100644 --- /dev/null +++ b/debian/changelog @@@ -1,0 -1,0 +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 --cc debian/control index 0000000,0000000..7ac5683 new file mode 100644 --- /dev/null +++ b/debian/control @@@ -1,0 -1,0 +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 --cc debian/copyright index 0000000,0000000..db047eb new file mode 100644 --- /dev/null +++ b/debian/copyright @@@ -1,0 -1,0 +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 --cc debian/patches/fix_gtest_depcheck.patch index 0000000,0000000..490d279 new file mode 100644 --- /dev/null +++ b/debian/patches/fix_gtest_depcheck.patch @@@ -1,0 -1,0 +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 --cc debian/patches/python3.patch index 0000000,0000000..b3795c5 new file mode 100644 --- /dev/null +++ b/debian/patches/python3.patch @@@ -1,0 -1,0 +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 --cc debian/patches/results_with_latest_samtools.patch index 0000000,0000000..8fa5af0 new file mode 100644 --- /dev/null +++ b/debian/patches/results_with_latest_samtools.patch @@@ -1,0 -1,0 +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 --cc debian/patches/series index 0000000,0000000..92ca5bd new file mode 100644 --- /dev/null +++ b/debian/patches/series @@@ -1,0 -1,0 +1,5 @@@ ++fix_gtest_depcheck.patch ++# debug_tests.patch ++use_debian_packaged_python3-cram.patch ++python3.patch ++results_with_latest_samtools.patch diff --cc debian/patches/use_debian_packaged_python3-cram.patch index 0000000,0000000..8a94cfc new file mode 100644 --- /dev/null +++ b/debian/patches/use_debian_packaged_python3-cram.patch @@@ -1,0 -1,0 +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 --cc debian/pbbamtools.install index 0000000,0000000..7380180 new file mode 100644 --- /dev/null +++ b/debian/pbbamtools.install @@@ -1,0 -1,0 +1,1 @@@ ++*/bin /usr diff --cc debian/rules index 0000000,0000000..684cf69 new file mode 100755 --- /dev/null +++ b/debian/rules @@@ -1,0 -1,0 +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 --cc debian/source/format index 0000000,0000000..163aaf8 new file mode 100644 --- /dev/null +++ b/debian/source/format @@@ -1,0 -1,0 +1,1 @@@ ++3.0 (quilt) diff --cc debian/tests/control index 0000000,0000000..9b21e04 new file mode 100644 --- /dev/null +++ b/debian/tests/control @@@ -1,0 -1,0 +1,5 @@@ ++Test-Command: debian/rules override_dh_auto_test ++Depends: ++ @builddeps@, ++ pbbamtools, ++Restrictions: rw-build-tree, allow-stderr diff --cc debian/watch index 0000000,0000000..1b64644 new file mode 100644 --- /dev/null +++ b/debian/watch @@@ -1,0 -1,0 +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@