public bool GetNextAlignment(Read read)
{
if (_bamReader == null)
{
throw new Exception("Already disposed.");
}
if (!_bamReader.GetNextAlignment(ref _rawAlignment, false) ||
(_bamIndexFilter > -1 && _rawAlignment.RefID != _bamIndexFilter))
{
Dispose();
return(false);
}
read.Reset(_bamReader.GetReferenceNameByID(_rawAlignment.RefID), _rawAlignment, _stitchReads);
return(true);
}
private List <Region> GetIntervalsForChr(int chrIndex)
{
if (_remainingIntervals != null)
{
var chrName = _bamReader.GetReferenceNameByID(chrIndex);
if (!_remainingIntervals.ContainsKey(chrName))
{
return new List <Region>()
{
new Region(1, 1)
}
}
; // return tiny interval of 1 so we essentially skip the chr
return(_remainingIntervals[chrName]);
}
return(null); // return null to signal that we shouldn't apply any interval optimization
}
