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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted 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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Code for writing BAM.
// ==========================================================================
#ifndef INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
#define INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
namespace seqan2 {
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function writeRecord() BamHeader
// ----------------------------------------------------------------------------
template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
void write(TTarget & target,
BamHeader const & header,
BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
Bam const & /*tag*/)
{
write(target, "BAM\1");
clear(context.buffer);
write(context.buffer, header, context, Sam());
// Note that we do not write out a null-character to terminate the header. This would be valid by the SAM standard
// but the samtools do not expect this and write out the '\0' when converting from BAM to SAM.
// appendValue(context.buffer, '\0');
// Write text header.
appendRawPod(target, static_cast<int32_t>(length(context.buffer)));
write(target, context.buffer);
// Write references.
if (!empty(context._contigNames))
{
int32_t nRef = _max(length(contigNames(context)), length(contigLengths(context)));
appendRawPod(target, nRef);
for (int32_t i = 0; i < nRef; ++i)
{
if (i < (int32_t)length(contigNames(context)))
{
appendRawPod(target, static_cast<int32_t>(length(contigNames(context)[i]) + 1));
write(target, contigNames(context)[i]);
}
else
{
appendRawPod(target, static_cast<int32_t>(1));
}
writeValue(target, '\0');
int32_t lRef = 0;
if (i < (int32_t)length(contigLengths(context)))
lRef = contigLengths(context)[i];
appendRawPod(target, lRef);
}
}
}
// ----------------------------------------------------------------------------
// Function writeRecord() BamAlignmentRecord
// ----------------------------------------------------------------------------
static inline int _reg2Bin(uint32_t beg, uint32_t end)
{
--end;
if (beg >> 14 == end >> 14)
return 4681 + (beg >> 14);
if (beg >> 17 == end >> 17)
return 585 + (beg >> 17);
if (beg >> 20 == end >> 20)
return 73 + (beg >> 20);
if (beg >> 23 == end >> 23)
return 9 + (beg >> 23);
if (beg >> 26 == end >> 26)
return 1 + (beg >> 26);
return 0;
}
inline uint32_t
updateLengths(BamAlignmentRecord const & record)
{
// update internal lengths.
record._l_qname = length(record.qName) + 1;
record._n_cigar = length(record.cigar);
record._l_qseq = length(record.seq);
return sizeof(BamAlignmentRecordCore) + record._l_qname +
record._n_cigar * 4 + (record._l_qseq + 1) / 2 + record._l_qseq +
length(record.tags);
}
template <typename TTarget>
inline void
_writeBamRecord(TTarget & target,
BamAlignmentRecord const & record,
Bam const & /*tag*/)
{
typedef typename Iterator<String<CigarElement<> > const, Standard>::Type SEQAN_RESTRICT TCigarIter;
typedef typename Iterator<IupacString const, Standard>::Type SEQAN_RESTRICT TSeqIter;
typedef typename Iterator<CharString const, Standard>::Type SEQAN_RESTRICT TQualIter;
// bin_mq_nl
unsigned l = 0;
_getLengthInRef(l, record.cigar);
record.bin =_reg2Bin(record.beginPos, record.beginPos + std::max(1u, l));
// Write fixed-size BamAlignmentRecordCore.
appendRawPod(target, (BamAlignmentRecordCore &)record);
// read_name
write(target, record.qName);
writeValue(target, '\0');
// cigar
static unsigned char const MAP[256] =
{
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0,
0, 0, 0, 0, 2, 0, 0, 0, 5, 1, 0, 0, 0, 0, 3, 0,
6, 0, 0, 4, 0, 0, 0, 0, 8, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
TCigarIter citEnd = end(record.cigar, Standard());
for (TCigarIter cit = begin(record.cigar, Standard()); cit != citEnd; ++cit)
appendRawPod(target, ((uint32_t)cit->count << 4) | MAP[(unsigned char)cit->operation]);
// seq
TSeqIter sit = begin(record.seq, Standard());
TSeqIter sitEnd = sit + (record._l_qseq & ~1);
while (sit != sitEnd)
{
unsigned char x = (ordValue(getValue(sit++)) << 4);
writeValue(target, x | ordValue(getValue(sit++)));
}
if (record._l_qseq & 1)
writeValue(target, ordValue(getValue(sit++)) << 4);
// qual
SEQAN_ASSERT_LEQ(length(record.qual), length(record.seq));
TQualIter qit = begin(record.qual, Standard());
TQualIter qitEnd = end(record.qual, Standard());
TQualIter qitVirtEnd = qit + record._l_qseq;
while (qit != qitEnd)
writeValue(target, *qit++ - '!');
for (; qit != qitVirtEnd; ++qit)
writeValue(target, '\xff'); // fill with zero qualities
// tags
write(target, record.tags);
}
template <typename TTarget>
inline void
_writeBamRecordWrapper(TTarget & target,
BamAlignmentRecord const & record,
Nothing & /* range */,
uint32_t size,
Bam const & tag)
{
appendRawPod(target, size);
_writeBamRecord(target, record, tag);
}
template <typename TTarget, typename TOValue>
inline void
_writeBamRecordWrapper(TTarget & target,
BamAlignmentRecord const & record,
Range<TOValue*> & range,
uint32_t size,
Bam const & tag)
{
if (SEQAN_LIKELY(size + 4 <= length(range)))
{
appendRawPod(range.begin, size);
_writeBamRecord(range.begin, record, tag);
advanceChunk(target, size + 4);
}
else
{
appendRawPod(target, size);
_writeBamRecord(target, record, tag);
}
}
template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
void write(TTarget & target,
BamAlignmentRecord const & record,
BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
Bam const & tag)
{
#ifdef SEQAN_DEBUG_OR_TEST_
// Check for valid IO Context.
if (record.rID != BamAlignmentRecord::INVALID_REFID)
{
SEQAN_ASSERT_LT_MSG(record.rID, static_cast<int32_t>(length(contigNames(context))),
"BAM IO Assertion: Unknown REF ID!");
}
if (record.rNextId != BamAlignmentRecord::INVALID_REFID)
{
SEQAN_ASSERT_LT_MSG(record.rNextId, static_cast<int32_t>(length(contigNames(context))),
"BAM IO Assertion: Unknown NEXT REF ID!");
}
#endif
ignoreUnusedVariableWarning(context);
// Update internal lengths
uint32_t size = updateLengths(record);
// Reserve chunk memory
reserveChunk(target, 4 + size, Output());
// Write length and record
typename Chunk<TTarget>::Type ochunk;
getChunk(ochunk, target, Output());
_writeBamRecordWrapper(target, record, ochunk, size, tag);
}
} // namespace seqan2
#endif // #ifndef INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
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