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sampe2se.cpp
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sampe2se.cpp
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// ==========================================================================
// SAMeval
// ==========================================================================
// Copyright (C) 2014 Enrico Siragusa, FU Berlin
//
// This program is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// This program is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
// more details.
//
// You should have received a copy of the GNU General Public License along
// with this program. If not, see <http://www.gnu.org/licenses/>.
//
// ==========================================================================
// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// ==========================================================================
#include <seqan/bam_io.h>
using namespace seqan;
// ============================================================================
// Functors
// ============================================================================
typedef EqualsChar<'.'> IsDot;
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function clearPairedFlags()
// ----------------------------------------------------------------------------
void clearPairedFlags(BamAlignmentRecord & record)
{
if (hasFlagMultiple(record))
record.flag = record.flag ^ BAM_FLAG_MULTIPLE;
if (hasFlagFirst(record))
record.flag = record.flag ^ BAM_FLAG_FIRST;
if (hasFlagLast(record))
record.flag = record.flag ^ BAM_FLAG_LAST;
if (hasFlagNextRC(record))
record.flag = record.flag ^ BAM_FLAG_NEXT_RC;
if (hasFlagNextUnmapped(record))
record.flag = record.flag ^ BAM_FLAG_NEXT_UNMAPPED;
if (hasFlagAllProper(record))
record.flag = record.flag ^ BAM_FLAG_ALL_PROPER;
}
// ----------------------------------------------------------------------------
// Function main()
// ----------------------------------------------------------------------------
int main(int argc, char ** argv)
{
if (argc != 3)
{
std::cerr << "usage: sampe2se <pe-bam> <se-bam>" << std::endl;
return 1;
}
BamFileIn bamFileIn;
BamFileOut bamFileOut(bamFileIn);
BamHeader header;
BamAlignmentRecord record;
if (!open(bamFileIn, toCString(argv[1])))
{
std::cerr << "Can't open the input file." << std::endl;
return 1;
}
if (!open(bamFileOut, toCString(argv[2])))
{
std::cerr << "Can't open the output file." << std::endl;
return 1;
}
readRecord(header, bamFileIn);
writeRecord(bamFileOut, header);
StringSet<CharString> qName;
while (!atEnd(bamFileIn))
{
readRecord(record, bamFileIn);
if (hasFlagFirst(record) || endsWith(record.qName, "/1"))
{
if (endsWith(record.qName, "/1"))
resize(record.qName, length(record.qName) - 2);
clear(qName);
strSplit(qName, record.qName, IsDot());
clear(record.qName);
append(record.qName, qName[0]);
appendValue(record.qName, '.');
appendValue(record.qName, 'L');
append(record.qName, qName[1]);
}
else if (hasFlagLast(record) || endsWith(record.qName, "/2"))
{
if (endsWith(record.qName, "/2"))
resize(record.qName, length(record.qName) - 2);
clear(qName);
strSplit(qName, record.qName, IsDot());
clear(record.qName);
append(record.qName, qName[0]);
appendValue(record.qName, '.');
appendValue(record.qName, 'R');
append(record.qName, qName[1]);
}
clearPairedFlags(record);
writeRecord(bamFileOut, record);
}
return 0;
}