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); }