public StitchingInfo GetStitchedCigar(CigarAlignment cigar1, int pos1, CigarAlignment cigar2, int pos2, bool reverseFirst, bool pairIsOutie)
{
var positions = GetStitchedSites(cigar1, cigar2, pos2, pos1);
var success = true;
var stitchingInfo = ReconcileSites(positions, reverseFirst, out success, pairIsOutie ? (int)cigar2.GetPrefixClip() : (int)cigar1.GetPrefixClip(), pairIsOutie ? (int)(cigar1.GetReadSpan() - (int)cigar1.GetSuffixClip()) : (int)(cigar2.GetReadSpan() - (int)cigar2.GetSuffixClip()), pairIsOutie);
return(success ? stitchingInfo : null);
}
public static uint GetReadSpanBetweenClippedEnds(this CigarAlignment cigar)
{
return(cigar.GetReadSpan() - cigar.GetPrefixClip() - cigar.GetSuffixClip());
}
public static CigarAlignment GetCigarWithoutProbeClips(this CigarAlignment cigar, bool isRead1)
{
return(isRead1 ?
cigar.GetSubCigar(cigar.GetPrefixClip() > 0 ? 1 : 0, cigar.Count) :
cigar.GetSubCigar(0, cigar.Count - (cigar.GetSuffixClip() > 0 ? 1 : 0)));
}
public static bool HasInternalSoftclip(this CigarAlignment cigar)
{
var subCigar = cigar.GetSubCigar(cigar.GetPrefixClip() > 0 ? 1 : 0, cigar.Count - (cigar.GetSuffixClip() > 0 ? 1 : 0));
foreach (CigarOp op in subCigar)
{
if (op.Type == 'S')
{
return(true);
}
}
return(false);
}
