[med-svn] [Git][med-team/pbbam][master] 6 commits: Adapt test results to latest samtools
Andreas Tille
gitlab at salsa.debian.org
Fri Dec 20 10:37:33 GMT 2019
Andreas Tille pushed to branch master at Debian Med / pbbam
Commits:
c92f00e3 by Andreas Tille at 2019-12-20T08:53:20Z
Adapt test results to latest samtools
- - - - -
fa8d989d by Andreas Tille at 2019-12-20T08:53:43Z
Refresh patch
- - - - -
b96eafdd by Andreas Tille at 2019-12-20T08:54:57Z
d-shlibs override for libpbcopper1.3.0-dev
- - - - -
02a6fa55 by Andreas Tille at 2019-12-20T09:11:52Z
Unfortunately upstream does not distinguishe between release version and SOVERSION - just follow their versioning anyway and rename dynamic library package
- - - - -
57cbce08 by Andreas Tille at 2019-12-20T10:26:57Z
Update d/copyright
- - - - -
b2fd7ff0 by Andreas Tille at 2019-12-20T10:32:54Z
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/python3.patch
- + debian/patches/results_with_latest_samtools.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-pbbam (1.0.6+dfsg-1) UNRELEASED; urgency=medium
+pbbam (1.0.6+dfsg-1) unstable; urgency=medium
* Drop <!nocheck> option from python3-cram
Closes: #934467
@@ -10,14 +10,13 @@ pbbam (1.0.6+dfsg-1) UNRELEASED; urgency=medium
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 distinguishe between release version
+ and SOVERSION - just follow their versioning anyway and rename
+ dynamic library package
- TODO: ... -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.0.6 -g -O2 -fdebug-prefix-map=/build/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbcopper -Wl,--end-group
- FAILED: src/libpbbam.so.1.0.6
- c++ -o src/libpbbam.so.1.0.6 'src/25a6634@@pbbam at sha/AlignmentPrinter.cpp.o' 'src/25a6634@@pbbam at sha/BaiIndexCache.cpp.o' 'src/25a6634@@pbbam at sha/BaiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam at sha/BamFile.cpp.o' 'src/25a6634@@pbbam at sha/BamFileMerger.cpp.o' 'src/25a6634@@pbbam at sha/BamHeader.cpp.o' 'src/25a6634@@pbbam at sha/BamReader.cpp.o' 'src/25a6634@@pbbam at sha/BamRecord.cpp.o' 'src/25a6634@@pbbam at sha/BamRecordBuilder.cpp.o' 'src/25a6634@@pbbam at sha/BamRecordImpl.cpp.o' 'src/25a6634@@pbbam at sha/BamRecordTags.cpp.o' 'src/25a6634@@pbbam at sha/BamRecordView.cpp.o' 'src/25a6634@@pbbam at sha/BamTagCodec.cpp.o' 'src/25a6634@@pbbam at sha/BamWriter.cpp.o' 'src/25a6634@@pbbam at sha/BarcodeQuery.cpp.o' 'src/25a6634@@pbbam at sha/BgzipFastaWriter.cpp.o' 'src/25a6634@@pbbam at sha/BgzipFastqWriter.cpp.o' 'src/25a6634@@pbbam at sha/BgzipWriter.cpp.o' 'src/25a6634@@pbbam at sha/ChemistryTable.cpp.o' 'src/25a6634@@pbbam at sha/Compare.cpp.o' 'src/25a6634@@pbbam at sha/CompositeFastaReader.cpp.o' 'src/25a6634@@pbbam at sha/Config.cpp.o' 'src/25a6634@@pbbam at sha/DataSet.cpp.o' 'src/25a6634@@pbbam at sha/DataSetBaseTypes.cpp.o' 'src/25a6634@@pbbam at sha/DataSetElement.cpp.o' 'src/25a6634@@pbbam at sha/DataSetIO.cpp.o' 'src/25a6634@@pbbam at sha/DataSetTypes.cpp.o' 'src/25a6634@@pbbam at sha/DataSetXsd.cpp.o' 'src/25a6634@@pbbam at sha/EntireFileQuery.cpp.o' 'src/25a6634@@pbbam at sha/FaiIndex.cpp.o' 'src/25a6634@@pbbam at sha/FaiZmwChunker.cpp.o' 'src/25a6634@@pbbam at sha/FastaCache.cpp.o' 'src/25a6634@@pbbam at sha/FastaReader.cpp.o' 'src/25a6634@@pbbam at sha/FastaSequence.cpp.o' 'src/25a6634@@pbbam at sha/FastaSequenceQuery.cpp.o' 'src/25a6634@@pbbam at sha/FastaWriter.cpp.o' 'src/25a6634@@pbbam at sha/FastqReader.cpp.o' 'src/25a6634@@pbbam at sha/FastqSequence.cpp.o' 'src/25a6634@@pbbam at sha/FastqWriter.cpp.o' 'src/25a6634@@pbbam at sha/FileProducer.cpp.o' 'src/25a6634@@pbbam at sha/FileUtils.cpp.o' 'src/25a6634@@pbbam at sha/FofnReader.cpp.o' 'src/25a6634@@pbbam at sha/FormatUtils.cpp.o' 'src/25a6634@@pbbam at sha/GenomicIntervalQuery.cpp.o' 'src/25a6634@@pbbam at sha/IFastaWriter.cpp.o' 'src/25a6634@@pbbam at sha/IFastqWriter.cpp.o' 'src/25a6634@@pbbam at sha/IndexedBamWriter.cpp.o' 'src/25a6634@@pbbam at sha/IndexedFastaReader.cpp.o' 'src/25a6634@@pbbam at sha/IndexedFastqBgzfReader.cpp.o' 'src/25a6634@@pbbam at sha/IndexedFastqReader.cpp.o' 'src/25a6634@@pbbam at sha/IndexedFastqTextReader.cpp.o' 'src/25a6634@@pbbam at sha/IndexedFastqReaderImpl.cpp.o' 'src/25a6634@@pbbam at sha/IRecordWriter.cpp.o' 'src/25a6634@@pbbam at sha/KSeqReader.cpp.o' 'src/25a6634@@pbbam at sha/MD5.cpp.o' 'src/25a6634@@pbbam at sha/MemoryUtils.cpp.o' 'src/25a6634@@pbbam at sha/PbiBuilder.cpp.o' 'src/25a6634@@pbbam at sha/PbiFile.cpp.o' 'src/25a6634@@pbbam at sha/PbiFilter.cpp.o' 'src/25a6634@@pbbam at sha/PbiFilterQuery.cpp.o' 'src/25a6634@@pbbam at sha/PbiFilterTypes.cpp.o' 'src/25a6634@@pbbam at sha/PbiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam at sha/PbiIndexIO.cpp.o' 'src/25a6634@@pbbam at sha/PbiRawData.cpp.o' 'src/25a6634@@pbbam at sha/ProgramInfo.cpp.o' 'src/25a6634@@pbbam at sha/QNameQuery.cpp.o' 'src/25a6634@@pbbam at sha/ReadAccuracyQuery.cpp.o' 'src/25a6634@@pbbam at sha/ReadGroupInfo.cpp.o' 'src/25a6634@@pbbam at sha/RecordType.cpp.o' 'src/25a6634@@pbbam at sha/SamTagCodec.cpp.o' 'src/25a6634@@pbbam at sha/SamWriter.cpp.o' 'src/25a6634@@pbbam at sha/SequenceInfo.cpp.o' 'src/25a6634@@pbbam at sha/StringUtilities.cpp.o' 'src/25a6634@@pbbam at sha/SubreadLengthQuery.cpp.o' 'src/25a6634@@pbbam at sha/Tag.cpp.o' 'src/25a6634@@pbbam at sha/TagCollection.cpp.o' 'src/25a6634@@pbbam at sha/TextFileReader.cpp.o' 'src/25a6634@@pbbam at sha/TextFileWriter.cpp.o' 'src/25a6634@@pbbam at sha/Validator.cpp.o' 'src/25a6634@@pbbam at sha/ValidationErrors.cpp.o' 'src/25a6634@@pbbam at sha/ValidationException.cpp.o' 'src/25a6634@@pbbam at sha/Version.cpp.o' 'src/25a6634@@pbbam at sha/VirtualZmwBamRecord.cpp.o' 'src/25a6634@@pbbam at sha/VirtualZmwCompositeReader.cpp.o' 'src/25a6634@@pbbam at sha/VirtualZmwReader.cpp.o' 'src/25a6634@@pbbam at sha/VirtualRegion.cpp.o' 'src/25a6634@@pbbam at sha/VirtualRegionTypeMap.cpp.o' 'src/25a6634@@pbbam at sha/XmlReader.cpp.o' 'src/25a6634@@pbbam at sha/XmlWriter.cpp.o' 'src/25a6634@@pbbam at sha/WhitelistedZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam at sha/ZmwChunkedFastaReader.cpp.o' 'src/25a6634@@pbbam at sha/ZmwChunkedFastqReader.cpp.o' 'src/25a6634@@pbbam at sha/ZmwChunkedFastxBgzfReader.cpp.o' 'src/25a6634@@pbbam at sha/ZmwChunkedFastxReaderImpl.cpp.o' 'src/25a6634@@pbbam at sha/ZmwChunkedFastxTextReader.cpp.o' 'src/25a6634@@pbbam at sha/ZmwGroupQuery.cpp.o' 'src/25a6634@@pbbam at sha/ZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam at sha/ZmwQuery.cpp.o' 'src/25a6634@@pbbam at sha/ZmwTypeMap.cpp.o' 'src/25a6634@@pbbam at sha/bed_BedReader.cpp.o' 'src/25a6634@@pbbam at sha/bed_BedWriter.cpp.o' 'src/25a6634@@pbbam at sha/ccs_CCSPbiBuilder.cpp.o' 'src/25a6634@@pbbam at sha/ccs_CCSRecordFormat.cpp.o' 'src/25a6634@@pbbam at sha/ccs_CCSRecordReader.cpp.o' 'src/25a6634@@pbbam at sha/ccs_CCSRecordWriter.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfFile.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfFormat.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfHeader.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfHeaderTypes.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfQuery.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfReader.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfSort.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfVariant.cpp.o' 'src/25a6634@@pbbam at sha/vcf_VcfWriter.cpp.o' 'src/25a6634@@pbbam at sha/pugixml_pugixml.cpp.o' -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.0.6 -g -O2 -fdebug-prefix-map=/build/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbcopper -Wl,--end-group
- /usr/bin/ld: cannot find -lpbcopper
- collect2: error: ld returned 1 exit status
-
- -- Andreas Tille <tille at debian.org> Fri, 13 Dec 2019 21:50:03 +0100
+ -- Andreas Tille <tille at debian.org> Fri, 20 Dec 2019 11:27:03 +0100
pbbam (0.23.0+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -27,7 +27,7 @@ Package: pbbamtools
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libpbbam0.23.0 (= ${binary:Version})
+ 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
@@ -42,7 +42,7 @@ Description: processing Pacific Biosciences binary alignment/map files
This package provides command-line utilities for working with PacBio BAM
files.
-Package: libpbbam0.23.0
+Package: libpbbam1.0.6
Architecture: any
Multi-Arch: same
Section: libs
@@ -65,7 +65,7 @@ Description: Pacific Biosciences binary alignment/map (BAM) library
Package: libpbbam-dev
Architecture: any
Section: libdevel
-Depends: libpbbam0.23.0 (= ${binary:Version}),
+Depends: libpbbam1.0.6 (= ${binary:Version}),
libhts-dev,
libssl-dev,
${misc:Depends}
=====================================
debian/copyright
=====================================
@@ -7,7 +7,7 @@ Files-Excluded: third-party
*/tests/scripts/cram*
Files: *
-Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet at pacificbiosciences.com>
+Copyright: 2014-2019 Pacific Biosciences of California, Inc. <devnet at pacificbiosciences.com>
License: PacBio-BSD-3-Clause
Files: src/pugixml/*
@@ -15,12 +15,9 @@ Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine at gmail.com>
2003 Kristen Wegner <kristen at tima.net>
License: MIT
-Files: tools/common/OptionParser.*
-Copyright: 2010 Johannes Weißl <jargon at molb.org>
-License: BSD-3-Clause or BSD-2-Clause
-
Files: debian/*
Copyright: 2015-2016 Afif Elghraoui <afif at debian.org>
+ 2016-2019 Andreas Tille <tille at debian.org>
License: PacBio-BSD-3-Clause
License: PacBio-BSD-3-Clause
@@ -52,55 +49,6 @@ License: PacBio-BSD-3-Clause
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
-License: BSD-3-Clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- 3. Neither the name of the University nor the names of its contributors
- may be used to endorse or promote products derived from this software
- without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE HOLDERS OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-License: BSD-2-Clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
- WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-
License: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
=====================================
debian/patches/python3.patch
=====================================
@@ -4,7 +4,7 @@ Description: Use Python3 in build time test suite
--- a/meson.build
+++ b/meson.build
-@@ -80,7 +80,7 @@ subdir('src')
+@@ -83,7 +83,7 @@ subdir('src')
if not meson.is_subproject()
if get_option('build-tools') or get_option('tests')
=====================================
debian/patches/results_with_latest_samtools.patch
=====================================
@@ -0,0 +1,250 @@
+Description: Adapt test results to latest samtools
+Author: Andreas Tille <tille at 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 $MERGED_BAM | grep -v 'CL:samtools view -H '
+ @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
+ @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
+ @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ fix_gtest_depcheck.patch
# debug_tests.patch
use_debian_packaged_python3-cram.patch
python3.patch
+results_with_latest_samtools.patch
=====================================
debian/rules
=====================================
@@ -56,6 +56,7 @@ override_dh_install:
--exclude-la \
--exclude-a \
--override s/libhts2-dev/libhts-dev/ \
+ --override s/libpbcopper1.3.0-dev/libpbcopper-dev/ \
--movedev debian/tmp/usr/include/* usr/include \
--movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
debian/tmp/usr/lib/*/*.so
View it on GitLab: https://salsa.debian.org/med-team/pbbam/compare/b6e675a36b85a43fff37848d5983d4847c08f14d...b2fd7ff0cf16a703918aa826b57e3b04ce51d739
--
View it on GitLab: https://salsa.debian.org/med-team/pbbam/compare/b6e675a36b85a43fff37848d5983d4847c08f14d...b2fd7ff0cf16a703918aa826b57e3b04ce51d739
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