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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2013, 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>
// ==========================================================================
// Iterate over BAM alignment, dump lines in SAM format, followed by the read
// alignment.
//
// USAGE: bam_print_alignments REF.fasta ALIGN.bam
// ==========================================================================
#include <iostream>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/file.h> // For printing SeqAn Strings.
#include <seqan/align.h>
#include <seqan/bam_io.h>
#include <seqan/seq_io.h>
#if SEQAN_HAS_ZLIB
void trimSeqHeaderToId(seqan::CharString & header)
{
unsigned i = 0;
for (; i < length(header); ++i)
if (isspace(header[i]))
break;
resize(header, i);
}
int main(int argc, char const ** argv)
{
using namespace seqan;
// Check command line arguments.
if (argc != 3)
{
std::cerr << "USAGE: bam_print_alignments REF.fasta FILE.bam" << std::endl;
return 1;
}
// Read FASTA file.
std::cerr << "Reading FASTA " << argv[1] << std::endl;
StringSet<CharString> refNameStore;
StringSet<Dna5String> seqs;
std::fstream inSeq(argv[1], std::ios::binary | std::ios::in);
if (!inSeq.good())
{
std::cerr << "Could not open FASTA file " << argv[1] << std::endl;
return 1;
}
RecordReader<std::fstream, SinglePass<> > reader(inSeq);
if (read2(refNameStore, seqs, reader, Fasta()) != 0)
return 1;
for (unsigned i = 0; i < length(refNameStore); ++i)
trimSeqHeaderToId(refNameStore[i]);
// Open BGZF stream.
std::cerr << "Opening BAM " << argv[2] << std::endl;
Stream<Bgzf> stream;
if (!open(stream, argv[2], "r"))
{
std::cerr << "[ERROR] Could not open BAM file" << argv[1] << std::endl;
return 1;
}
// Read Header.
std::cerr << "Reading Header" << std::endl;
NameStoreCache<StringSet<CharString> > refNameStoreCache(refNameStore);
BamIOContext<StringSet<CharString> > context(refNameStore, refNameStoreCache);
BamHeader header;
if (readRecord(header, context, stream, Bam()) != 0)
{
std::cerr << "[ERROR] Could not read header from BAM file!" << std::endl;
return 1;
}
// Stream through file, getting alignment and dumping it.
std::cerr << "Reading Alignments..." << std::endl;
Align<Dna5String> align;
BamAlignmentRecord record;
while (!atEnd(stream))
{
clear(record);
if (readRecord(record, context, stream, Bam()) != 0)
{
std::cerr << "[ERROR] Error reading alignment!" << std::endl;
return 1;
}
if (record.rID == BamAlignmentRecord::INVALID_REFID)
continue; // Skip * reference.
// Convert BAM record to alignment.
bamRecordToAlignment(align, seqs[record.rID], record);
// Dump record as SAM and the alignment.
write2(std::cout, record, context, Sam());
std::cout << align << std::endl;
}
return 0;
}
#else // #if SEQAN_HAS_ZLIB
int main()
{
std::cerr << "zlib is required for bam_print_alignment demo." << std::endl;
return 1;
}
#endif // #if SEQAN_HAS_ZLIB
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