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// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// 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:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * 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.
//
// * 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.
// Author: Derek Barnett
#include "pbbam/SamWriter.h"
#include "pbbam/Validator.h"
#include "FileProducer.h"
#include "MemoryUtils.h"
#include <htslib/hfile.h>
#include <htslib/sam.h>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace std;
namespace PacBio {
namespace BAM {
namespace internal {
class SamWriterPrivate : public internal::FileProducer
{
public:
SamWriterPrivate(const std::string& filename,
const PBBAM_SHARED_PTR<bam_hdr_t> rawHeader)
: internal::FileProducer(filename)
, file_(nullptr)
, header_(rawHeader)
{
if (!header_)
throw std::runtime_error("null header");
// open file
const string& usingFilename = TempFilename();
const string& mode = string("w");
file_.reset(sam_open(usingFilename.c_str(), mode.c_str()));
if (!file_)
throw std::runtime_error("could not open file for writing");
// write header
const int ret = sam_hdr_write(file_.get(), header_.get());
if (ret != 0)
throw std::runtime_error("could not write header");
}
void TryFlush(void);
void Write(const BamRecord& record);
private:
std::unique_ptr<samFile, internal::HtslibFileDeleter> file_;
PBBAM_SHARED_PTR<bam_hdr_t> header_;
};
void SamWriterPrivate::TryFlush(void)
{
const auto ret = file_.get()->fp.hfile;
if (ret != 0)
throw std::runtime_error("could not flush output buffer contents");
}
void SamWriterPrivate::Write(const BamRecord& record)
{
#if PBBAM_AUTOVALIDATE
Validator::Validate(record);
#endif
const auto rawRecord = internal::BamRecordMemory::GetRawData(record);
// store bin number
// min_shift=14 & n_lvls=5 are SAM/BAM "magic numbers"
rawRecord->core.bin = hts_reg2bin(rawRecord->core.pos,
bam_endpos(rawRecord.get()), 14, 5);
// write record to file
const int ret = sam_write1(file_.get(), header_.get(), rawRecord.get());
if (ret <= 0)
throw std::runtime_error("could not write record");
}
} // namespace internal
} // namespace BAM
} // namespace PacBio
SamWriter::SamWriter(const string& filename, const BamHeader& header)
: IRecordWriter()
, d_(nullptr)
{
#if PBBAM_AUTOVALIDATE
Validator::Validate(header);
#endif
d_.reset(new internal::SamWriterPrivate{ filename,
internal::BamHeaderMemory::MakeRawHeader(header)
});
}
SamWriter::~SamWriter(void) { }
void SamWriter::TryFlush(void)
{
d_->TryFlush();
}
void SamWriter::Write(const BamRecord& record)
{
d_->Write(record);
}
void SamWriter::Write(const BamRecordImpl& recordImpl)
{
d_->Write( BamRecord{recordImpl} );
}
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