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);
}
/// <summary>
/// Unpacks the sequence so that it is aligned to the reference at the given start but ignoring insertions.
/// Useful for Depth of Coverage;
/// </summary>
public void ProcessCountCoverageFromSequence(CompactSAMSequence orgSeq)
{
if (orgSeq == null || orgSeq.RName != StaticResources.MT_CHROMOSOME_NAME)
{
return;
}
string CIGAR = orgSeq.CIGAR;
if (!CigarUtils.NoInformationCigar(CIGAR))
{
int curRef = orgSeq.Pos - 1;
var elements = CigarUtils.GetCigarElements(CIGAR);
foreach (var v in elements)
{
var len = v.Length;
switch (v.Operation)
{
case 'P': //padding (Silent deltions from padded reference)
case 'N': //skipped region from reference
throw new Exception("Not built to handle clipping yet");
case 'M': //match or mismatch
case '=': //match
case 'X': //mismatch
for (int k = 0; k < len; k++)
{
if (curRef >= StaticResources.CRS_LENGTH)
{
Debug.WriteLine("Seq: " + orgSeq.ID + " is aligned past the MT DNA reference genome");
break;
}
depthCounts [curRef] = depthCounts [curRef] + 1.0;
curRef++;
}
break;
case 'I': //insertion to the reference
break;
case 'D': //Deletion from the reference
curRef += len;
break;
case 'S': //soft clipped
case 'H': //had clipped
break;
default:
throw new FormatException("Unexpected SAM Cigar element found " + v.Operation.ToString());
}
}
}
}
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;
}
/// <summary>
/// Gets the reference sequence alignment length depending on the CIGAR value.
/// </summary>
/// <returns>Length of the alignment.</returns>
private int getRefSeqAlignmentLengthFromCIGAR()
{
if (CigarUtils.NoInformationCigar(CIGAR))
{
return(0);
}
var elements = CigarUtils.GetCigarElements(CIGAR);
int len = 0;
foreach (var v in elements)
{
if (CigarUtils.CigarElementis_MDNX_Equal(v.Operation))
{
len += v.Length;
}
}
return(len);
}
