private void UpdateFromBam()
{
if (BamAlignment.CigarData != null)
{
ValidateCigar(BamAlignment.CigarData, BamAlignment.Bases.Length);
}
_stitchedCigarInitialized = _directionCigarInitialized = _sequencedBaseDirectionMapInitialized = _positionMapInitialized = false;
_isDuplex = null;
_directionCigar = null;
_sequencedBaseDirectionMap = null;
}
private void GetDirectionCigarFromBam()
{
if (BamAlignment.TagData != null && BamAlignment.TagData.Length > 0)
{
var xdTag = BamAlignment.GetStringTag("XD");
if (xdTag != null)
{
_directionCigar = new CigarDirection(xdTag);
}
_directionCigarInitialized = true;
}
}
public static DirectionType[] CreateSequencedBaseDirectionMap(CigarDirection directionCigar, CigarAlignment cigarData)
{
var cigarBaseDirectionMap = directionCigar.Expand();;
var cigarBaseAlleleMap = cigarData.Expand();
var sequencedBaseDirectionMap = new DirectionType[cigarData.GetReadSpan()];
int sequencedBaseIndex = 0;
for (int cigarBaseIndex = 0; cigarBaseIndex < cigarBaseDirectionMap.Count; cigarBaseIndex++)
{
var cigarOp = cigarBaseAlleleMap[cigarBaseIndex];
if (cigarOp.IsReadSpan()) //choices: (MIDNSHP)
{
sequencedBaseDirectionMap[sequencedBaseIndex] = cigarBaseDirectionMap[cigarBaseIndex];
sequencedBaseIndex++;
}
}
return(sequencedBaseDirectionMap);
}
public CigarDirectionExpander(CigarDirection cigarDirection)
{
_cigarDirection = cigarDirection;
_cigarIndex = 0;
_opIndex = 0;
}