private bool ReadIsDuplicate(BamAlignment alignment)
{
if (_dupIdentifier.IsDuplicate(alignment))
{
_statusCounter.AddStatusCount("Duplicates");
return(_skipDuplicates);
}
return(false);
}
public List <BamAlignment> ExtractReads(ReadPair pair)
{
const char Forward = 'F';
const char Reverse = 'R';
var reads = new List <BamAlignment>();
var chrom1 = _refIdMapping[pair.Read1.RefID];
var chrom2 = _refIdMapping[pair.Read2.RefID];
var alignmentSet = new AlignmentSet(
new Read(chrom1, pair.Read1),
new Read(chrom2, pair.Read2),
false);
var read1dir = pair.Read1.IsReverseStrand() ? Reverse : Forward;
var read2dir = pair.Read2.IsReverseStrand() ? Reverse : Forward;
if (pair.Read1.IsSecondMate())
{
read1dir = pair.Read2.IsReverseStrand() ? Reverse : Forward;
read2dir = pair.Read1.IsReverseStrand() ? Reverse : Forward;
}
bool stitched = false;
if (_tryStitch)
{
stitched = _stitcher.TryStitch(alignmentSet);
}
if (stitched)
{
//_statusCounter.AddStatusCount("Stitched");
if (alignmentSet.ReadsForProcessing.Count > 1)
{
throw new InvalidDataException("AlignmentSets for stitched reads should only have one ReadsForProcessing.");
}
foreach (var read in alignmentSet.ReadsForProcessing)
{
var alignment = StitcherHelpers.StitchifyBamAlignment(pair, read, read1dir, read2dir);
reads.Add(alignment);
}
}
else
{
if (!_filterUnstitchablePairs)
{
//_statusCounter.AddStatusCount("Unstitchable Pairs Kept");
reads.Add(new BamAlignment(alignmentSet.PartnerRead1.BamAlignment));
reads.Add(new BamAlignment(alignmentSet.PartnerRead2.BamAlignment));
}
else
{
_statusCounter.AddStatusCount("Unstitchable Pairs Filtered");
}
}
return(reads);
}
private void AddStatus(string status)
{
_readStatuses.AddStatusCount(status);
}
public void AddStatusCount(string status)
{
_statusCounter.AddStatusCount(status);
}
public List <BamAlignment> ExtractReads(ReadPair pair)
{
var reads = new List <BamAlignment>();
var chrom1 = _refIdMapping[pair.Read1.RefID];
var chrom2 = _refIdMapping[pair.Read2.RefID];
var alignmentSet = new AlignmentSet(
new Read(chrom1, pair.Read1),
new Read(chrom2, pair.Read2),
false);
var stitched = _stitcher.TryStitch(alignmentSet);
if (stitched)
{
if (alignmentSet.ReadsForProcessing.Count > 1)
{
throw new Exception("AlignmentSets for stitched reads should only have one ReadsForProcessing.");
}
foreach (var read in alignmentSet.ReadsForProcessing)
{
var alignment = new BamAlignment(read.BamAlignment);
alignment.SetIsFirstMate(false);
alignment.SetIsProperPair(false);
var tagUtils = new TagUtils();
if (read.StitchedCigar != null)
{
alignment.CigarData = read.StitchedCigar;
}
if (read.CigarDirections != null)
{
tagUtils.AddStringTag("XD", read.CigarDirections.ToString());
}
var tagData = tagUtils.ToBytes();
var existingTags = alignment.TagData;
if (existingTags == null)
{
alignment.TagData = tagData;
}
else
{
alignment.AppendTagData(tagData);
}
reads.Add(alignment);
}
}
else
{
if (!_filterUnstitchablePairs)
{
_statusCounter.AddStatusCount("Unstitchable Pairs Kept");
reads.Add(new BamAlignment(alignmentSet.PartnerRead1.BamAlignment));
reads.Add(new BamAlignment(alignmentSet.PartnerRead2.BamAlignment));
}
else
{
_statusCounter.AddStatusCount("Unstitchable Pairs Filtered");
}
}
return(reads);
}