public static bool HasSupplementaryAlignment(this BamAlignment alignment)
{
if (alignment.TagData == null)
{
return(false);
}
var saTag = alignment.GetStringTag("SA");
return(saTag != null);
}
public static List <BamAlignment> GetSupplementaryAlignments(this BamAlignment alignment, Dictionary <string, int> refIdMapping = null)
{
var supplementaries = new List <BamAlignment>();
if (!alignment.HasSupplementaryAlignment())
{
return(supplementaries);
}
var tag = alignment.GetStringTag("SA");
var supplementaryAlignments = tag.Split(new[] { ';' }, StringSplitOptions.RemoveEmptyEntries);
foreach (var supplementaryAlignment in supplementaryAlignments)
{
// SA tag format: (rname,pos,strand,CIGAR,mapQ,NM ;)+
var splitTag = supplementaryAlignment.Split(new[] { ',' }, StringSplitOptions.RemoveEmptyEntries);
var tagChromosome = splitTag[0];
var tagPosition = int.Parse(splitTag[1]);
var tagStrand = splitTag[2];
var tagCigar = splitTag[3];
var tagMapq = splitTag[4];
var tagNM = splitTag[5];
var bamAlignment = new BamAlignment()
{
Position = tagPosition - 1, // Deal with the fact that BamAlignment obj is 0-indexed, whereas SA is 1-indexed
CigarData = new CigarAlignment(tagCigar),
};
if (tagStrand == "-")
{
bamAlignment.SetIsReverseStrand(true);
}
if (refIdMapping != null)
{
Console.WriteLine(tagChromosome);
bamAlignment.RefID = refIdMapping[tagChromosome];
}
supplementaries.Add(bamAlignment);
}
return(supplementaries);
}