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_NoXC_Unstitchable()
{
var read1 = TestHelper.CreateRead("chr1", "ATCGATCG", 12345, new CigarAlignment("8M"), qualityForAll: 30);
var read2_noOverlap = TestHelper.CreateRead("chr1", "A", 2384, new CigarAlignment("1M"), qualityForAll: 30);
var read2_overlap = TestHelper.CreateRead("chr1", "ATCGTT", 12349, new CigarAlignment("6M"), qualityForAll: 30);
var read2_diffChrom = TestHelper.CreateRead("chr2", "ATCGTT", 12349, new CigarAlignment("6M"), qualityForAll: 30);
var read2_nonOverlap_border = TestHelper.CreateRead("chr1", "AT", 12343, new CigarAlignment("2M"), qualityForAll: 30);
var stitcher = StitcherTestHelpers.GetStitcher(10, true);
// -----------------------------------------------
// Either of the partner reads is missing*
// *(only read that could be missing is read 2, if read 1 was missing couldn't create alignment set)
// -----------------------------------------------
// Should throw an exception
var alignmentSet = new AlignmentSet(read1, null);
Assert.Throws <ArgumentException>(() => stitcher.TryStitch(alignmentSet));
// -----------------------------------------------
// No overlap, reads are far away
// -----------------------------------------------
// Shouldn't stitch
alignmentSet = new AlignmentSet(read1, read2_noOverlap);
StitcherTestHelpers.TryStitchAndAssertFailed(stitcher, alignmentSet);
// -----------------------------------------------
// No overlap, reads are directly neighboring
// -----------------------------------------------
// Shouldn't stitch
alignmentSet = new AlignmentSet(read1, read2_nonOverlap_border);
StitcherTestHelpers.TryStitchAndAssertFailed(stitcher, alignmentSet);
// -----------------------------------------------
// No overlap, reads on diff chromosomes
// -----------------------------------------------
// Should throw exception
alignmentSet = new AlignmentSet(read1, read2_diffChrom);
var ex = Assert.Throws <ArgumentException>(() => stitcher.TryStitch(alignmentSet));
Assert.Contains("Partner reads are from different chromosomes", ex.Message, StringComparison.InvariantCultureIgnoreCase); // This is brittle but since a variety of exceptions can happen in this process want to make sure it's this specific one
}
public static void TestSuccesfullyStitchedRead(Read read1, Read read2, int minQscore, string xcTag, Action <Read> assertions)
{
var alignmentSet = new AlignmentSet(read1, read2);
var stitcher = StitcherTestHelpers.GetStitcher(minQscore);
stitcher.TryStitch(alignmentSet);
// -----------------------------------------------
// Basic Stitcher, No XC tag
// -----------------------------------------------
CheckMergedRead(xcTag, assertions, alignmentSet);
// -----------------------------------------------
// XC Stitcher (XC Req), No XC tag
// -----------------------------------------------
alignmentSet = new AlignmentSet(read1, read2);
stitcher = StitcherTestHelpers.GetStitcher(minQscore, true);
StitcherTestHelpers.TryStitchAndAssertFailed(stitcher, alignmentSet);
// -----------------------------------------------
// Basic Stitcher, With XC tag
// -----------------------------------------------
read1.StitchedCigar = new CigarAlignment(xcTag);
read2.StitchedCigar = new CigarAlignment(xcTag);
alignmentSet = new AlignmentSet(read1, read2);
stitcher = StitcherTestHelpers.GetStitcher(minQscore);
stitcher.TryStitch(alignmentSet);
CheckMergedRead(xcTag, assertions, alignmentSet);
// -----------------------------------------------
// XC Stitcher (XC Req), With XC tag
// -----------------------------------------------
alignmentSet = new AlignmentSet(read1, read2);
stitcher = StitcherTestHelpers.GetStitcher(minQscore, true);
stitcher.TryStitch(alignmentSet);
CheckMergedRead(xcTag, assertions, alignmentSet);
}
public void TryStitch_CalculateStitchedCigar()
{
// -----------------------------------------------
// Read position maps disagree
// -----------------------------------------------
var read1 = TestHelper.CreateRead("chr1", "ATCGATCG", 12345, new CigarAlignment("2M2D3M1D3M"), qualityForAll: 30);
var read2 = TestHelper.CreateRead("chr1", "ATCGATCG", 12349, new CigarAlignment("8M"), qualityForAll: 30);
// [If require XC]
// We never calculate stitched cigar anyway. Bounce out to processing separately.
var stitcher = GetXCStitcher();
var alignmentSet = new AlignmentSet(read1, read2);
StitcherTestHelpers.TryStitchAndAssertFailed(stitcher, alignmentSet);
// -----------------------------------------------
// When calculating stitched cigar, stitched cigar should have
// - everything from read1 before the overlap
// - everything from read2 starting from the overlap
// But since we ensure that the position maps agree in the overlap region, it's really not a matter of one taking precedence over the other
// 1234... 1 - - 2 3 4 5 6 - - 7 8 9 0
// Read1 X X X X X X X X - - - - -
// Read1 M I I M M M M M - - - - -
// Read2 - - - X X X X X X X X - -
// Read2 - - - M M M M M I M M - -
// -----------------------------------------------
// [If require XC]
// No stitched cigar, and separate reads
read1 = TestHelper.CreateRead("chr1", "ATCGATCG", 12341, new CigarAlignment("1M2I5M"), qualityForAll: 30);
read2 = TestHelper.CreateRead("chr1", "ATCGATCG", 12342, new CigarAlignment("5M1I2M"), qualityForAll: 30);
stitcher = GetXCStitcher();
alignmentSet = new AlignmentSet(read1, read2);
StitcherTestHelpers.TryStitchAndAssertFailed(stitcher, 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);
}
