public BamReaderContainer(Stream inStream, string filename)
{
_bamReader = new BamReader();
_bamReader.Open(inStream);
_filename = filename;
_currentBamAlignment = new BamAlignment();
_currentSerializedAlignment = new SerializedBamAlignment();
MoveToNextRecord();
}
/// <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");
}