public CompactSAMSequence CreateTrimmedSequence(int newLength)
{
if (newLength > this.sequenceData.Length || newLength < 1)
{
throw new ArgumentOutOfRangeException("length");
}
byte[] newSequenceData = new byte[newLength];
sbyte[] newQualityScores = new sbyte[newLength];
Array.Copy(sequenceData, 0, newSequenceData, 0, newLength);
Array.Copy(qualityScores, 0, newQualityScores, 0, newLength);
//now to adjust cigar
string newCigar = CIGAR;
if (!CigarUtils.NoInformationCigar(CIGAR))
{
var elements = CigarUtils.GetCigarElements(CIGAR);
int curLen = 0;
for (int i = 0; i < elements.Count; i++)
{
var ce = elements [i];
var op = ce.Operation;
if (op == CigarOperations.HARD_CLIP || op == CigarOperations.DELETION)
{
continue;
}
else if (op == CigarOperations.PADDING || op == CigarOperations.SKIPPED)
{
throw new NotImplementedException();
}
else if (op == CigarOperations.SOFT_CLIP || op == CigarOperations.INSERTION || CigarOperations.OperationIsMatch(op))
{
curLen += ce.Length;
if (curLen == newLength)
{
newCigar = CigarUtils.CreateCigarString(elements.Take(i + 1));
break;
}
else if (curLen > newLength)
{
var dif = curLen - newLength;
ce.Length -= dif;
elements [i] = ce;
newCigar = CigarUtils.CreateCigarString(elements.Take(i + 1));
break;
}
}
}
}
var ns = new CompactSAMSequence(this.Alphabet, this.FormatType, newSequenceData, newQualityScores, false);
ns.Pos = Pos;
ns.CIGAR = newCigar;
return(ns);
}
public void TrimSequence(int newLength)
{
Count = newLength;
if (newLength > this.sequenceData.Length || newLength < 1)
{
throw new ArgumentOutOfRangeException("length");
}
Array.Resize(ref sequenceData, newLength);
Array.Resize(ref qualityScores, newLength);
//now to adjust cigar
string newCigar = CIGAR;
if (!CigarUtils.NoInformationCigar(CIGAR))
{
var elements = CigarUtils.GetCigarElements(CIGAR);
int curLen = 0;
for (int i = 0; i < elements.Count; i++)
{
var ce = elements [i];
var op = ce.Operation;
if (op == CigarOperations.HARD_CLIP || op == CigarOperations.DELETION)
{
continue;
}
else if (op == CigarOperations.PADDING || op == CigarOperations.SKIPPED)
{
throw new NotImplementedException();
}
else if (op == CigarOperations.SOFT_CLIP || op == CigarOperations.INSERTION || CigarOperations.OperationIsMatch(op))
{
curLen += ce.Length;
if (curLen == newLength)
{
newCigar = CigarUtils.CreateCigarString(elements.Take(i + 1));
break;
}
else if (curLen > newLength)
{
ce.Length -= curLen - newLength;
elements [i] = ce;
newCigar = CigarUtils.CreateCigarString(elements.Take(i + 1));
break;
}
}
}
}
CIGAR = newCigar;
}