public void TryStitch_NoXC_Stitchable()
{
//Reads without XC tags that do overlap should be added as one merged read in basic stitcher
var basicStitcher = StitcherTestHelpers.GetStitcher(10);
var alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
basicStitcher.TryStitch(alignmentSet);
Assert.Equal(1, alignmentSet.ReadsForProcessing.Count);
}
public void TryStitch_NoXC_Stitchable()
{
var xcStitcherXcRequired = GetXCStitcher();
//Reads without XC tags that do overlap should be added separately in XC stitcher when xc is required
var alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
StitcherTestHelpers.TryStitchAndAssertFailed(xcStitcherXcRequired, alignmentSet);
}
public void TryStitch_WithXCTag()
{
const string xcTagDiffFromCalculated = "4M2I4M";
const string expectedCalculatedCigar = "10M";
var xcRequiredStitcher = GetXCStitcher();
// -----------------------------------------------
// XC tag is available, and matching between R1 and R2, and expected length,
// but is different from the cigar string we would have calculated
// -----------------------------------------------
// [If require XC]
// XC tag should be taken
var alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
alignmentSet.PartnerRead1.StitchedCigar = new CigarAlignment(xcTagDiffFromCalculated);
alignmentSet.PartnerRead2.StitchedCigar = new CigarAlignment(xcTagDiffFromCalculated);
xcRequiredStitcher.TryStitch(alignmentSet);
Assert.Equal(1, alignmentSet.ReadsForProcessing.Count);
var mergedRead = alignmentSet.ReadsForProcessing.First();
Assert.Equal(xcTagDiffFromCalculated, mergedRead.CigarData.ToString());
// -----------------------------------------------
// XC tag is there, and matching between R1 and R2, but not expected length
// -----------------------------------------------
// [If not require XC]
//bounce back to processing separately?
//alignmentSet = GetOverlappingReadSet();
//alignmentSet.PartnerRead1.StitchedCigarString = "8M";
//alignmentSet.PartnerRead2.StitchedCigarString = "8M";
//stitcher.TryStitch(alignmentSet);
//Assert.Equal(2, alignmentSet.ReadsForProcessing.Count);
// [If require XC]
//???
// -----------------------------------------------
// XC tag is there on one read but not the other
// -----------------------------------------------
// [If require XC]
// should bounce back to separate processing
alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
alignmentSet.PartnerRead1.StitchedCigar = new CigarAlignment("4M2I4M");
alignmentSet.PartnerRead2.StitchedCigar = null;
StitcherTestHelpers.TryStitchAndAssertFailed(xcRequiredStitcher, alignmentSet);
alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
alignmentSet.PartnerRead1.StitchedCigar = null;
alignmentSet.PartnerRead2.StitchedCigar = new CigarAlignment("4M2I4M");
StitcherTestHelpers.TryStitchAndAssertFailed(xcRequiredStitcher, alignmentSet);
// -----------------------------------------------
// XC tag is not there
// -----------------------------------------------
// [If require XC]
// should bounce back to separate processing
alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
alignmentSet.PartnerRead1.StitchedCigar = null;
alignmentSet.PartnerRead2.StitchedCigar = null;
StitcherTestHelpers.TryStitchAndAssertFailed(xcRequiredStitcher, alignmentSet);
// -----------------------------------------------
// XC tag does not match between read1 and read2
// -----------------------------------------------
// [If require XC]
// should bounce back to separate processing
alignmentSet = StitcherTestHelpers.GetOverlappingReadSet();
alignmentSet.PartnerRead1.StitchedCigar = new CigarAlignment("4M2I4M");
alignmentSet.PartnerRead2.StitchedCigar = new CigarAlignment("9M1I");
StitcherTestHelpers.TryStitchAndAssertFailed(xcRequiredStitcher, alignmentSet);
}
