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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));
}
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