public PileUp(string rname, BaseAndQualityAndPosition bqp)
{
this.RName = rname;
this.Position = bqp.Position;
this.Bases = new List <BaseAndQuality>(DEFAULT_LIST_SIZE);
this.Bases.Add(bqp.BaseWithQuality);
this.InsertionOffSet = bqp.InsertionOffSet;
}
public PileUp(string rname, BaseAndQualityAndPosition bqp)
{
this.RName = rname;
this.Position = bqp.Position;
this.Bases = new List<BaseAndQuality>(DEFAULT_LIST_SIZE);
this.Bases.Add(bqp.BaseWithQuality);
this.InsertionOffSet = bqp.InsertPositionPassedRefPosition;
}
List<BaseAndQualityAndPosition> getBasesForSequence(SAMAlignedSequence seq)
{
List<BaseAndQualityAndPosition> toReturn = new List<BaseAndQualityAndPosition>(seq.RefEndPos - seq.Pos + 10);
// Decode the cigar string into operations.
// TODO: This code is duplicated in many places
string CIGAR = seq.CIGAR;
List<KeyValuePair<char, int>> charsAndPositions = new List<KeyValuePair<char, int>>();
for (int i = 0; i < CIGAR.Length; i++)
{
char ch = CIGAR[i];
if (Char.IsDigit(ch))
{
continue;
}
charsAndPositions.Add(new KeyValuePair<char, int>(ch, i));
}
// Get sequence bases and error probabilities
var qseq = seq.QuerySequence as QualitativeSequence;
var seq_log10ErrorProb = qseq.GetPhredQualityScores().Select(Utils.GetLog10ErrorProbability).ToArray();
var seq_bases = qseq.ToArray();
// Use the cigar operations to emit bases.
int curRef = seq.Pos;
int curQuery = 0;
for (int i = 0; i < charsAndPositions.Count; i++)
{
// Parse the current cigar operation
char ch = charsAndPositions[i].Key;
int cig_start = i==0 ? 0 : charsAndPositions[i - 1].Value + 1;
int cig_end = charsAndPositions[i].Value - cig_start;
int cig_len = int.Parse(CIGAR.Substring(cig_start, cig_end));
// Emit or advance based on cigar operation.
switch (ch)
{
case 'P': //padding (Silent deltions from padded reference)
case 'N': //skipped region from reference
throw new Exception("Pile up methods not built to handle reference clipping (Cigar P or N) yet.");
case 'M': //match or mismatch
case '=': //match
case 'X': //mismatch
for (int k = 0; k < cig_len; k++)
{
var bqp= new BaseAndQualityAndPosition(curRef,0, new BaseAndQuality(seq_bases[curQuery], seq_log10ErrorProb[curQuery]));
toReturn.Add(bqp);
curQuery++;
curRef++;
}
break;
case 'I'://insertion to the reference
for (int k = 0; k < cig_len; k++)
{
var bqp = new BaseAndQualityAndPosition(curRef,k, new BaseAndQuality(seq_bases[curQuery], seq_log10ErrorProb[curQuery]));
toReturn.Add(bqp);
curQuery++;
}
break;
case 'D'://Deletion from the reference
for (int k = 0; k < cig_len; k++)
{
var bqp = new BaseAndQualityAndPosition(curRef,k, new BaseAndQuality((byte)'-', Double.NaN));
toReturn.Add(bqp);
curRef++;
}
break;
case 'S': //soft clipped
curQuery += cig_len;
break;
case 'H'://had clipped
break;
default:
throw new FormatException("Unexpected SAM Cigar element found " + ch.ToString());
}
}
return toReturn;
}
