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);
}
public void GetSubCigar()
{
var cigar = new CigarAlignment("2S3M1D1M");
var subCigar = cigar.GetSubCigar(0, cigar.Count - 1);
Assert.Equal("2S3M1D", subCigar.ToString());
subCigar = cigar.GetSubCigar(0, cigar.Count);
Assert.Equal("2S3M1D1M", subCigar.ToString());
subCigar = cigar.GetSubCigar(1, cigar.Count);
Assert.Equal("3M1D1M", subCigar.ToString());
subCigar = cigar.GetSubCigar(1, cigar.Count - 1);
Assert.Equal("3M1D", subCigar.ToString());
subCigar = cigar.GetSubCigar(2, 2);
Assert.Equal("", subCigar.ToString());
Assert.Throws <ArgumentException>(() => cigar.GetSubCigar(3, 2));
}
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)));
}