[med-svn] [Git][med-team/pbseqlib][master] 4 commits: d/patches/pbbam_2.3.0: adapt to changes in pbbam 2.3.0 / pbcopper 2.2.0
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Aug 22 19:49:22 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / pbseqlib
Commits:
7dde8b3d by Michael R. Crusoe at 2023-08-22T20:39:56+02:00
d/patches/pbbam_2.3.0: adapt to changes in pbbam 2.3.0 / pbcopper 2.2.0
- - - - -
2f9e56df by Michael R. Crusoe at 2023-08-22T20:40:40+02:00
d/control: add missing ${devlibs:Depends} to libblasr-dev
- - - - -
52af243f by Michael R. Crusoe at 2023-08-22T20:47:34+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
37c3c318 by Michael R. Crusoe at 2023-08-22T20:47:40+02:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/pbbam_2.3.0
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+pbseqlib (5.3.5+dfsg-6) unstable; urgency=medium
+
+ * Team upload.
+ * debian/patches/pbbam_2.3.0: adapt to changes in pbbam 2.3.0
+ & pbcopper 2.2.0
+ * d/control: add missing ${devlibs:Depends} to libblasr-dev
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 22 Aug 2023 20:47:40 +0200
+
pbseqlib (5.3.5+dfsg-5) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -13,10 +13,10 @@ Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
libhdf5-dev,
libboost-dev,
- libpbbam-dev,
- libpbcopper-dev,
- libhts-dev,
-Standards-Version: 4.6.0
+ libpbbam-dev (>> 2.3.0),
+ libpbcopper-dev (>> 2.2.0),
+ libhts-dev
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/pbseqlib
Vcs-Git: https://salsa.debian.org/med-team/pbseqlib.git
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
@@ -28,9 +28,8 @@ Multi-Arch: same
Section: libdevel
Depends: libblasr5.3.5 (= ${binary:Version}),
libpbdata-dev (= ${binary:Version}),
+ ${devlibs:Depends},
${misc:Depends}
-Breaks: libblasr (<< 5.3.3)
-Replaces: libblasr (<< 5.3.3)
Description: tools for aligning PacBio reads to target sequences (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
@@ -81,10 +80,10 @@ Description: library for analyzing PacBio sequencing data (development files)
Package: libpbdata-dev
Architecture: any
+Multi-Arch: same
Section: libdevel
Depends: ${misc:Depends},
libpbcopper-dev
-Multi-Arch: same
Description: tools for handling PacBio sequences (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
=====================================
debian/patches/pbbam_2.3.0
=====================================
@@ -0,0 +1,182 @@
+Author: Michael R. Crusoe
+Description: Adapt to pbbam 2.3.0 / pbcopper 2.2.0 changes
+--- pbseqlib.orig/hdf/HDFPulseCallsWriter.cpp
++++ pbseqlib/hdf/HDFPulseCallsWriter.cpp
+@@ -4,6 +4,7 @@
+
+ #include <hdf/HDFPulseCallsWriter.hpp>
+ #include <pbdata/utils/TimeUtils.hpp>
++#include <pbcopper/data/QualityValues.h>
+
+ #include <algorithm>
+ #include <cctype>
+@@ -354,7 +355,7 @@
+ {
+ if (HasLabelQV()) {
+ if (read.HasLabelQV()) {
+- const PacBio::BAM::QualityValues& qvs = read.LabelQV();
++ const PacBio::Data::QualityValues& qvs = read.LabelQV();
+ std::vector<uint8_t> data(qvs.cbegin(), qvs.cend());
+ _CheckRead(read, data.size(), "LabelQV");
+ labelQVArray_.Write(&data[0], data.size());
+@@ -395,7 +396,7 @@
+ {
+ if (HasPulseMergeQV()) {
+ if (read.HasPulseMergeQV()) {
+- const PacBio::BAM::QualityValues& qvs = read.PulseMergeQV();
++ const PacBio::Data::QualityValues& qvs = read.PulseMergeQV();
+ std::vector<uint8_t> data(qvs.cbegin(), qvs.cend());
+ _CheckRead(read, data.size(), "PulseMergeQV");
+ pulseMergeQVArray_.Write(&data[0], data.size());
+@@ -476,7 +477,7 @@
+ {
+ if (HasAltLabelQV()) {
+ if (read.HasAltLabelQV()) {
+- const PacBio::BAM::QualityValues& qvs = read.AltLabelQV();
++ const PacBio::Data::QualityValues& qvs = read.AltLabelQV();
+ std::vector<uint8_t> data(qvs.begin(), qvs.end());
+ _CheckRead(read, data.size(), "AltLabelQV");
+ altLabelQVArray_.Write(&data[0], data.size());
+--- pbseqlib.orig/alignment/datastructures/alignment/FilterCriteria.cpp
++++ pbseqlib/alignment/datastructures/alignment/FilterCriteria.cpp
+@@ -18,6 +18,8 @@
+
+ #include <alignment/datastructures/alignment/FilterCriteria.hpp>
+ #include <pbdata/PrettyException.hpp>
++#include <pbcopper/data/Orientation.h>
++#include <pbcopper/data/Cigar.h>
+
+ constexpr float Score::errorunit;
+
+@@ -374,26 +376,26 @@
+ {
+ assert(record.IsMapped() and record.Impl().HasTag(AS));
+ DNALength alnLength = static_cast<DNALength>(
+- record.Sequence(PacBio::BAM::Orientation::NATIVE, true, true).size());
+- PacBio::BAM::Cigar cigar = record.CigarData();
++ record.Sequence(PacBio::Data::Orientation::NATIVE, true, true).size());
++ PacBio::Data::Cigar cigar = record.CigarData();
+
+ uint32_t nMatch = 0, nMismatch = 0, nIns = 0, nDel = 0;
+ for (auto op : cigar) {
+ uint32_t n = op.Length();
+ switch (op.Type()) {
+- case PacBio::BAM::CigarOperationType::SEQUENCE_MATCH:
++ case PacBio::Data::CigarOperationType::SEQUENCE_MATCH:
+ nMatch += n;
+ break;
+- case PacBio::BAM::CigarOperationType::SEQUENCE_MISMATCH:
++ case PacBio::Data::CigarOperationType::SEQUENCE_MISMATCH:
+ nMismatch += n;
+ break;
+- case PacBio::BAM::CigarOperationType::ALIGNMENT_MATCH:
++ case PacBio::Data::CigarOperationType::ALIGNMENT_MATCH:
+ nMismatch += n;
+ break;
+- case PacBio::BAM::CigarOperationType::INSERTION:
++ case PacBio::Data::CigarOperationType::INSERTION:
+ nIns += n;
+ break;
+- case PacBio::BAM::CigarOperationType::DELETION:
++ case PacBio::Data::CigarOperationType::DELETION:
+ nDel += n;
+ break;
+ default:
+--- pbseqlib.orig/pbdata/SMRTSequence.cpp
++++ pbseqlib/pbdata/SMRTSequence.cpp
+@@ -3,6 +3,8 @@
+ #include <pbdata/PrettyException.hpp>
+ #include <pbdata/SMRTSequence.hpp>
+ #include <pbdata/utils/SMRTTitle.hpp>
++#include <pbcopper/data/Orientation.h>
++#include <pbcopper/data/Strand.h>
+
+ #include <cstdlib>
+
+@@ -435,8 +437,8 @@
+ void SMRTSequence::MakeNativeOrientedBamRecord(const PacBio::BAM::BamRecord &record)
+ {
+ bamRecord = PacBio::BAM::BamRecord(record); // copy first
+- if (record.IsMapped() and record.AlignedStrand() == PacBio::BAM::Strand::REVERSE) {
+- PacBio::BAM::BamRecordView bv(record, PacBio::BAM::Orientation::NATIVE, false, false);
++ if (record.IsMapped() and record.AlignedStrand() == PacBio::Data::Strand::REVERSE) {
++ PacBio::BAM::BamRecordView bv(record, PacBio::Data::Orientation::NATIVE, false, false);
+ bamRecord.Impl().Flag(PacBio::BAM::BamRecordImpl::UNMAPPED); // set flag as unmapped
+ bamRecord.Impl().SetSequenceAndQualities(bv.Sequence(), bv.Qualities().Fastq());
+ if (bamRecord.HasInsertionQV()) bamRecord.InsertionQV(bv.InsertionQVs());
+--- pbseqlib.orig/alignment/format/BAMPrinterImpl.hpp
++++ pbseqlib/alignment/format/BAMPrinterImpl.hpp
+@@ -6,6 +6,9 @@
+ #include <algorithm>
+
+ #include <pbdata/utils/SMRTTitle.hpp>
++#include <pbcopper/data/Cigar.h>
++#include <pbcopper/data/Strand.h>
++#include <pbcopper/data/Position.h>
+
+ using namespace BAMOutput;
+
+@@ -41,7 +44,7 @@
+ CreateCIGARString(alignment, read, cigarString, clipping, prefixSoftClip, suffixSoftClip,
+ prefixHardClip, suffixHardClip, cigarUseSeqMatch, allowAdjacentIndels);
+ SetAlignedSequence(alignment, read, alignedSequence, clipping);
+- PacBio::BAM::Cigar cigar = PacBio::BAM::Cigar::FromStdString(cigarString);
++ PacBio::Data::Cigar cigar = PacBio::Data::Cigar::FromStdString(cigarString);
+
+ // build flag
+ uint16_t flag;
+@@ -52,15 +55,15 @@
+ seqString.assign((char *)alignedSequence.seq, alignedSequence.length);
+
+ // Get alignment starting position on reference sequence forward strand.
+- PacBio::BAM::Position pos = 0;
+- PacBio::BAM::Strand strand;
++ PacBio::Data::Position pos = 0;
++ PacBio::Data::Strand strand;
+ if (alignment.tStrand == 0) {
+- pos = static_cast<PacBio::BAM::Position>(alignment.TAlignStart());
+- strand = PacBio::BAM::Strand::FORWARD;
++ pos = static_cast<PacBio::Data::Position>(alignment.TAlignStart());
++ strand = PacBio::Data::Strand::FORWARD;
+ } else {
+- pos = static_cast<PacBio::BAM::Position>(alignment.tLength -
++ pos = static_cast<PacBio::Data::Position>(alignment.tLength -
+ (alignment.TAlignStart() + alignment.TEnd()));
+- strand = PacBio::BAM::Strand::REVERSE;
++ strand = PacBio::Data::Strand::REVERSE;
+ }
+
+ if (buildFromScratch) {
+@@ -75,12 +78,12 @@
+ bamRecord.Impl().Bin(0);
+ bamRecord.Impl().InsertSize(0);
+ bamRecord.Impl().MapQuality(static_cast<uint8_t>(alignment.mapQV));
+- bamRecord.Impl().MatePosition(static_cast<PacBio::BAM::Position>(-1));
++ bamRecord.Impl().MatePosition(static_cast<PacBio::Data::Position>(-1));
+ bamRecord.Impl().MateReferenceId(static_cast<int32_t>(-1));
+ bamRecord.Impl().Position(pos);
+ bamRecord.Impl().ReferenceId(static_cast<int32_t>(alignment.tIndex));
+
+- if (strand == PacBio::BAM::Strand::REVERSE) {
++ if (strand == PacBio::Data::Strand::REVERSE) {
+ bamRecord.Impl().SetReverseStrand(true);
+ }
+
+@@ -136,14 +139,14 @@
+ bamRecord.Impl().CigarData(cigar);
+ } else {
+ // The following code can be used to hard-clip reads, if needed.
+- // PacBio::BAM::Position clipStart = read.bamRecord.QueryStart() + alignment.QAlignStart();
+- // PacBio::BAM::Position clipEnd = read.bamRecord.QueryStart() + alignment.QAlignEnd();
++ // PacBio::Data::Position clipStart = read.bamRecord.QueryStart() + alignment.QAlignStart();
++ // PacBio::Data::Position clipEnd = read.bamRecord.QueryStart() + alignment.QAlignEnd();
+ // bamRecord = PacBio::BAM::BamRecord::Clipped(read.bamRecord,
+ // PacBio::BAM::ClipType::CLIP_TO_QUERY,
+ // clipStart, clipEnd).
+ bamRecord = PacBio::BAM::BamRecord::Mapped(subread.bamRecord,
+ static_cast<int32_t>(alignment.tIndex),
+- static_cast<PacBio::BAM::Position>(pos), strand,
++ static_cast<PacBio::Data::Position>(pos), strand,
+ cigar, static_cast<uint8_t>(alignment.mapQV));
+ }
+
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ hdf5-1.10.0-support.patch
meson.patch
static+shared_lib.patch
gcc-13.patch
+pbbam_2.3.0
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/compare/f5f7baac654c5446799a9de2c52d36351b925e0e...37c3c318145947dc1c2d217b87bd81f7e71b3044
--
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/compare/f5f7baac654c5446799a9de2c52d36351b925e0e...37c3c318145947dc1c2d217b87bd81f7e71b3044
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