Batch::RunStatus PairedEndBatch::parseAlignmentFile(void) {
// open reader on new BAM alignment file
BamTools::BamReader reader;
if ( !reader.Open(m_generatedBam) ) {
m_errorString = "could not open generated BAM file: ";
m_errorString.append(m_generatedBam);
m_errorString.append(" to parse alignments");
return Batch::Error;
}
// set up data containers
m_result.ReadLengths.reserve(2 * m_settings->BatchSize);
m_result.FragmentLengths.reserve(m_settings->BatchSize);
// plow through alignments
BamTools::BamAlignment mate1;
BamTools::BamAlignment mate2;
while ( reader.GetNextAlignmentCore(mate1) ) {
// store mate1 read length, regardless of aligned state
m_result.ReadLengths.push_back(mate1.Length);
// read mate2
if ( reader.GetNextAlignmentCore(mate2) ) {
// store mate2 read length, regardless of aligned state
m_result.ReadLengths.push_back(mate2.Length);
// if both mates mapped to same reference
if ( mate1.IsMapped() &&
mate2.IsMapped() &&
(mate1.RefID == mate2.RefID) )
{
// calculate & store fragment length
m_result.FragmentLengths.push_back( calculateFragmentLength(mate1, mate2) );
}
}
}
reader.Close();
// remove extreme outliers
removeOutliers(m_result.FragmentLengths);
removeOutliers(m_result.ReadLengths);
// if we get here, all should be OK
return Batch::Normal;
}
