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);
}
public static void TryStitchAndAssertFailed(IAlignmentStitcher stitcher, AlignmentSet alignmentSet)
{
Assert.False(stitcher.TryStitch(alignmentSet).Stitched);
}
public static void TryStitchAndAssertAddedSeparately(IAlignmentStitcher stitcher, AlignmentSet alignmentSet)
{
Assert.True(stitcher.TryStitch(alignmentSet).Stitched);
Assert.True(alignmentSet.ReadsForProcessing.Contains(alignmentSet.PartnerRead1));
Assert.True(alignmentSet.ReadsForProcessing.Contains(alignmentSet.PartnerRead2));
}
public AlignmentSet GetNextAlignmentSet()
{
while (true)
{
if (!_alignmentExtractor.GetNextAlignment(_read))
{
Logger.WriteToLog("Totals: {0} reads processed, {1} reads skipped, {2} read pairs unstitchable.", _totalReadsReturned, _totalSkipped, _unstitchablePairs);
return(null); // no more reads
}
_lastReadPosition = _read.Position;
if (ShouldSkipRead(_read))
{
_totalSkipped++;
continue;
}
if (!_read.IsProperPair || _mateFinder == null)
{
_totalReadsReturned++;
return(new AlignmentSet(_read, null, true));
}
var origMate = _mateFinder.GetMate(_read);
if (origMate != null)
{
var alignmentSet = new AlignmentSet(origMate, _read);
try
{
if (_stitcher != null)
{
_stitcher.TryStitch(alignmentSet);
}
else
{
alignmentSet.ReadsForProcessing.Add(alignmentSet.PartnerRead1);
alignmentSet.ReadsForProcessing.Add(alignmentSet.PartnerRead2);
}
_totalReadsReturned += 2;
return(alignmentSet);
}
catch (ReadsNotStitchableException ex)
{
_unstitchablePairs++;
//For now go back to processing reads separately if they are unstitchable
alignmentSet.ReadsForProcessing.Add(alignmentSet.PartnerRead1);
alignmentSet.ReadsForProcessing.Add(alignmentSet.PartnerRead2);
_totalReadsReturned += 2;
return(alignmentSet);
//if (Constants.DebugMode)
// Logger.WriteToLog(
// string.Format("Unable to stitch reads '{0}' and '{1}'. Will skip pair. Error: {2}",
// origMate, alignment, ex.Message));
}
}
}
}
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);
}
public static void TryStitchAndAssertFailed(IAlignmentStitcher stitcher, AlignmentSet alignmentSet)
{
Assert.Throws <ReadsNotStitchableException>(() => stitcher.TryStitch(alignmentSet));
}