// Read an alignment pair from the BamReader.
// Returns false if the read fails
bool readAlignmentPair(BamTools::BamReader* pReader,
BamTools::BamAlignment& record1,
BamTools::BamAlignment& record2)
{
// Read a pair from the BAM
// Read record 1. Skip secondary alignments of the previous pair
do
{
if(!pReader->GetNextAlignment(record1))
return false;
} while(!record1.IsPrimaryAlignment());
// Read record 2.
do
{
if(!pReader->GetNextAlignment(record2))
return false;
} while(!record2.IsPrimaryAlignment());
return true;
}
uint32_t BamAlignmentReader::GetReadLength(const std::string& bamPath)
{
uint32_t bamReadLength = 300;
BamTools::BamReader bamReader;
if (!bamReader.Open(bamPath))
{
throw "Unable to open bam file";
}
BamTools::BamAlignment bamAlignment;
while(bamReader.GetNextAlignment(bamAlignment))
{
if (bamAlignment.IsPrimaryAlignment())
{
bamReadLength = bamAlignment.QueryBases.size();
break;
}
}
bamReader.Close();
return bamReadLength;
}