/// <summary>
/// Creates an index from a specified BAM file
/// </summary>
public void CreateIndexFromBamFile(string filename)
{
_numUnalignedWithoutCoordinates = 0;
// open the BAM file and retrieve the reference data
using (BamReader reader = new BamReader(filename))
{
// allocate space for the reference index
List <GenomeMetadata.SequenceMetadata> references = reader.GetReferences();
// iterate over all of the reads in the BAM file
Initialize(references.Count, reader.Tell());
BamAlignment al = new BamAlignment();
while (reader.GetNextAlignment(ref al, true))
{
if (!UpdateReferenceIndex(ref al, reader.Tell()))
{
break;
}
}
// perform some post-processing on the index
PostProcessing(reader.Tell());
if (_hasUnalignedReads)
{
while (reader.GetNextAlignment(ref al, true))
{
++_numUnalignedWithoutCoordinates;
}
}
}
// write the index to a file
WriteIndex(filename + ".bai");
}
public override void MoveToNextRecord()
{
_isEnd = !_bamReader.GetNextAlignment(ref _currentBamAlignment, false);
if (_isEnd)
{
return;
}
// No memory allocation
_currentSerializedAlignment.RefID = _currentBamAlignment.RefID;
_currentSerializedAlignment.Position = _currentBamAlignment.Position;
_currentSerializedAlignment.AlignmentFlag = _currentBamAlignment.AlignmentFlag;
_currentSerializedAlignment.FragmentLength = _currentBamAlignment.FragmentLength;
_currentSerializedAlignment.MapQuality = _currentBamAlignment.MapQuality;
_currentSerializedAlignment.MatePosition = _currentBamAlignment.MatePosition;
_currentSerializedAlignment.MateRefID = _currentBamAlignment.MateRefID;
_currentSerializedAlignment.IsReverseStrand = _currentBamAlignment.IsReverseStrand();
_currentSerializedAlignment.Name = _currentBamAlignment.Name;
}