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#include "PbbamInternalConfig.h"
#include <pbbam/IndexedFastqReader.h>
#include <pbbam/BamRecord.h>
#include <pbbam/FaiIndex.h>
#include <pbbam/FormatUtils.h>
#include "IndexedFastqBgzfReader.h"
#include "IndexedFastqReaderImpl.h"
#include "IndexedFastqTextReader.h"
#include "SequenceUtils.h"
#include <pbcopper/data/GenomicInterval.h>
#include <sstream>
#include <stdexcept>
#include <utility>
#include <cassert>
namespace PacBio {
namespace BAM {
namespace {
void ClipAndGapify(std::pair<std::string, Data::QualityValues>& seqQual, const Data::Cigar& cigar,
bool exciseSoftClips)
{
auto& subseq = seqQual.first;
auto subQual = seqQual.second.Fastq();
const char nullQual = Data::QualityValue{0}.Fastq();
size_t seqIndex = 0;
for (const auto& op : cigar) {
const auto type = op.Type();
const auto opLength = op.Length();
// do nothing for hard clips
if (type == Data::CigarOperationType::HARD_CLIP) {
continue;
}
// maybe remove soft clips
if (type == Data::CigarOperationType::SOFT_CLIP) {
if (!exciseSoftClips) {
subseq.reserve(subseq.size() + opLength);
subseq.insert(seqIndex, opLength, '-');
subQual.reserve(subQual.size() + opLength);
subQual.insert(seqIndex, opLength, nullQual);
seqIndex += opLength;
}
}
// for non-clipping operations
else {
// maybe add gaps/padding
if (type == Data::CigarOperationType::INSERTION) {
subseq.reserve(subseq.size() + opLength);
subseq.insert(seqIndex, opLength, '-');
subQual.reserve(subseq.size() + opLength);
subQual.insert(seqIndex, opLength, nullQual);
} else if (type == Data::CigarOperationType::PADDING) {
subseq.reserve(subseq.size() + opLength);
subseq.insert(seqIndex, opLength, '*');
subQual.reserve(subseq.size() + opLength);
subQual.insert(seqIndex, opLength, nullQual);
}
// update index
seqIndex += opLength;
}
}
seqQual.second = Data::QualityValues::FromFastq(subQual);
}
std::unique_ptr<IndexedFastqReaderImpl> MakeReaderImpl(std::string filename)
{
// validate extension
if (!FormatUtils::IsFastqFilename(filename)) {
std::ostringstream s;
s << "[pbbam] FASTQ reader ERROR: not a recognized FASTQ extension:\n"
<< " file: " << filename;
throw std::runtime_error{s.str()};
}
// determine subsequence "loader" from compression type: plain-text, bgzf, or unsupported
const auto compressionType = FormatUtils::CompressionType(filename);
switch (compressionType) {
case HtslibCompression::NONE:
return std::make_unique<IndexedFastqTextReader>(std::move(filename));
case HtslibCompression::BGZIP:
return std::make_unique<IndexedFastqBgzfReader>(std::move(filename));
case HtslibCompression::GZIP: {
std::ostringstream msg;
msg << "[pbbam] FASTQ reader ERROR: random-access is not supported for plain gzipped "
"file "
<< filename << "\n\n"
<< "Compressed files must be bgzipped, with accompanying *.gzi "
"index.\n\n"
<< "To keep the original gzipped file unchanged:\n"
<< " $ gunzip -c " << filename << " > <unzipped_file>\n"
<< "or discard the gzipped file:\n"
<< " $ gunzip " << filename << '\n'
<< '\n'
<< "Re-compress & create *.gzi index:\n"
<< " $ bgzip --index <unzipped_file>\n\n";
throw std::runtime_error{msg.str()};
}
default: {
assert(false); // should never get here, the way htslib currently determines type
std::ostringstream s;
s << "[pbbam] FASTQ reader ERROR: could not determine compression type:\n"
<< " file: " << filename;
throw std::runtime_error{s.str()};
}
}
}
} // namespace
IndexedFastqReader::IndexedFastqReader(std::string filename)
: d_{MakeReaderImpl(std::move(filename))}
{}
IndexedFastqReader::IndexedFastqReader(const IndexedFastqReader& other)
: d_{MakeReaderImpl(other.d_->faiFilename_)}
{}
IndexedFastqReader::IndexedFastqReader(IndexedFastqReader&&) noexcept = default;
IndexedFastqReader& IndexedFastqReader::operator=(const IndexedFastqReader& rhs)
{
if (this != &rhs) {
*this = IndexedFastqReader{rhs};
}
return *this;
}
IndexedFastqReader& IndexedFastqReader::operator=(IndexedFastqReader&&) noexcept = default;
IndexedFastqReader::~IndexedFastqReader() = default;
bool IndexedFastqReader::HasSequence(const std::string& name) const
{
return d_->index_.HasEntry(name);
}
std::vector<std::string> IndexedFastqReader::Names() const { return d_->index_.Names(); }
std::string IndexedFastqReader::Name(const size_t idx) const { return d_->index_.Names().at(idx); }
int IndexedFastqReader::NumSequences() const { return d_->index_.Names().size(); }
std::pair<std::string, Data::QualityValues> IndexedFastqReader::ReferenceSubsequence(
const BamRecord& bamRecord, const Data::Orientation orientation, const bool gapped,
const bool exciseSoftClips)
{
// fetch raw data for record's region
auto seqQual = Subsequence(bamRecord.ReferenceName(), bamRecord.ReferenceStart(),
bamRecord.ReferenceEnd());
// maybe clip/gapify
if (bamRecord.Impl().IsMapped() && gapped) {
ClipAndGapify(seqQual, bamRecord.Impl().CigarData(), exciseSoftClips);
}
// maybe reverse
const auto reverse =
(orientation != Data::Orientation::GENOMIC) && bamRecord.Impl().IsReverseStrand();
if (reverse) {
ReverseComplementCaseSens(seqQual.first);
Reverse(seqQual.second);
}
return seqQual;
}
int IndexedFastqReader::SequenceLength(const std::string& name) const
{
const auto& entry = d_->index_.Entry(name);
return static_cast<int>(entry.Length);
}
std::pair<std::string, Data::QualityValues> IndexedFastqReader::Subsequence(const std::string& id,
Data::Position start,
Data::Position end)
{
return d_->Subsequence(id, start, end);
}
std::pair<std::string, Data::QualityValues> IndexedFastqReader::Subsequence(
const Data::GenomicInterval& interval)
{
return Subsequence(interval.Name(), interval.Start(), interval.Stop());
}
} // namespace BAM
} // namespace PacBio
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