public void TestHomoPolymerScenario(Read read1, Read read2, Read mergedRead, bool useSoftClippedBases, bool expectedResult)
{
var alignmentSet = new AlignmentSet(read1, read2);
var basicStitcher = new BasicStitcher(10, useSoftclippedBases: useSoftClippedBases);
Assert.Equal(expectedResult, basicStitcher.TryStitch(alignmentSet));
//Assert.Equal(expectedResult, OverlapEvaluator.BridgeAnchored(mergedRead));
}
public void RunStitchingScenarios(StitchingScenario scenario, string resultFile)
{
Console.WriteLine(scenario.Category + " " + scenario.Id);
bool resultLogged = false;
try
{
var stitcher = new BasicStitcher(10);
var inputRead1 = scenario.InputRead1.ToRead();
var inputRead2 = scenario.InputRead2.ToRead();
var alignmentSet = new AlignmentSet(inputRead1, inputRead2);
var didStitch = stitcher.TryStitch(alignmentSet);
LogResult(resultFile, scenario, didStitch, alignmentSet);
resultLogged = true;
if (scenario.ShouldStitch)
{
Assert.Equal(scenario.ShouldStitch, didStitch);
Assert.True(OutputDirectionsMatch(scenario, alignmentSet));
Assert.True(OutputCigarsMatch(scenario, alignmentSet));
}
if (didStitch)
{
// TODO fix scenario source files so we can turn this back on.
Assert.True(OutputCigarsMatch(scenario, alignmentSet));
}
}
catch (Exception ex)
{
if (!resultLogged)
{
LogResult(resultFile, scenario, false, null, message: "Threw exception: " + ex.Message);
}
throw;
}
}
public void TryStitch_RealExamples()
{
// Real example from Kristina's problematic variant #73
var read1Bases =
"GAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGCAGCTCATCACGCAGCTCATGCCCTTCGG";
var read2Bases =
"AGGAAGCCTTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGCAGCTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACACAAAG";
var read1 = DomainTestHelper.CreateRead("chr7", read1Bases, 55248972, new CigarAlignment("20S9M12I109M"));
var read2 = DomainTestHelper.CreateRead("chr7", read2Bases, 55248981, new CigarAlignment("9S120M21S"));
StitcherTestHelpers.SetReadDirections(read2, DirectionType.Reverse);
var stitcher = new BasicStitcher(10, useSoftclippedBases: false);
var alignmentSet = new AlignmentSet(read1, read2);
stitcher.TryStitch(alignmentSet);
var mergedRead = StitcherTestHelpers.GetMergedRead(alignmentSet);
Assert.Equal("20S9M12I120M21S", mergedRead.CigarData.ToString());
Assert.Equal("41F109S32R", mergedRead.CigarDirections.ToString());
// Shouldn't stitch - problem Yu was having (tried to merge and then said the base at position 158 is null).
read1Bases =
"CGACGCTCTTGCGATCTTCAAAGCAATAGGATGGGTGATCAGGGATGTTGCTTACAAGAAAAGAACTGCCATACAGCTTCAACAACAACTTCTTCCACCCACCCCTAAAATGATGCTAAAAAGTAAGTCATCTCTGGTTCTCCCCCGATT";
read2Bases =
"TCAAAGCAATAGGATGGATGATCAGAGATGTTGCTTACAAGAAAAGAACTGCCATACAGCTTCAACAACAACTTCTTCCACTCCCCCCTAAAGTGATGCTAAAAAGTAAATCATCCCTGTTTCTCCCCCGTTCGCGAATTTCTACGATCG";
read1 = DomainTestHelper.CreateRead("chr7", read1Bases, 109465121, new CigarAlignment("44S56M1I23M26S"));
read2 = DomainTestHelper.CreateRead("chr7", read2Bases, 109465121, new CigarAlignment("27S55M1I24M43S"));
StitcherTestHelpers.SetReadDirections(read2, DirectionType.Reverse);
stitcher = new BasicStitcher(10, useSoftclippedBases: true);
alignmentSet = new AlignmentSet(read1, read2);
Assert.False(stitcher.TryStitch(alignmentSet));
}
public void TryStitch_ReCo()
{
// Real example from ReCo, was failing to generate the correct stitched cigar
var read1Bases =
"GTACTCCTACAGTCCCACCCCTCCCCTATAAACCTTATGAATCCCCGTTCACTTAGATGCCAGCTTGGCAAGGAAGGGAAGTACACATCTGTTGACAGTAATGAAATATCCTTGATAAGGATTTAAATTTTGGATGTGCTG";
var read2Bases =
"ACCTACAGTCCCACCCCTCCCCTATAAACCTTAGGAATCCCCGTTCACTTAGATGCCAGCTTGGCAAGGAAGGGAAGTACACATCTGTTGACAGTAATGAAATATCCTTGATAAGGATTTAAATTTTGGATGTGCTGAGCT";
// 8 9
// 3 4 5 6 7 8 9 0 1 2
// s s s s s M M M M M ...
// - - - - M M M M M M ...
// F F F F R S S S S S ... // Stitched directions if we don't allow softclip to contribute
// F F F F S S S S S S ... // Stitched directions if we do allow softclip to contribute
var read1 = DomainTestHelper.CreateRead("chr21", read1Bases, 16685488,
new CigarAlignment("5S136M"));
var read2 = DomainTestHelper.CreateRead("chr21", read2Bases, 16685487,
new CigarAlignment("137M4S"));
StitcherTestHelpers.SetReadDirections(read2, DirectionType.Reverse);
var stitcher = new BasicStitcher(10, useSoftclippedBases: false);
var alignmentSet = new AlignmentSet(read1, read2);
stitcher.TryStitch(alignmentSet);
// Without allowing softclips to count to support, should still get a M at an M/S overlap, but it won't be stitched.
var mergedRead = StitcherTestHelpers.GetMergedRead(alignmentSet);
Assert.Equal("4S137M4S", mergedRead.CigarData.ToString());
var expectedDirections = StitcherTestHelpers.BuildDirectionMap(new List <IEnumerable <DirectionType> >
{
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Forward, 4),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Reverse, 1),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Stitched, 136),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Reverse, 4)
});
StitcherTestHelpers.VerifyDirectionType(expectedDirections, mergedRead.CigarDirections.Expand().ToArray());
stitcher = new BasicStitcher(10, useSoftclippedBases: true);
alignmentSet = new AlignmentSet(read1, read2);
stitcher.TryStitch(alignmentSet);
mergedRead = StitcherTestHelpers.GetMergedRead(alignmentSet);
Assert.Equal("4S137M4S", mergedRead.CigarData.ToString());
expectedDirections = StitcherTestHelpers.BuildDirectionMap(new List <IEnumerable <DirectionType> >
{
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Forward, 4),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Reverse, 1),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Stitched, 136),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Reverse, 4)
});
StitcherTestHelpers.VerifyDirectionType(expectedDirections, mergedRead.CigarDirections.Expand().ToArray());
// If we're not ignoring probe softclips, go back to the original expected directions (1 more stitched from probe)
stitcher = new BasicStitcher(10, useSoftclippedBases: true, ignoreProbeSoftclips: false);
alignmentSet = new AlignmentSet(read1, read2);
stitcher.TryStitch(alignmentSet);
mergedRead = StitcherTestHelpers.GetMergedRead(alignmentSet);
Assert.Equal("4S137M4S", mergedRead.CigarData.ToString());
expectedDirections = StitcherTestHelpers.BuildDirectionMap(new List <IEnumerable <DirectionType> >
{
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Forward, 4),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Stitched, 137),
StitcherTestHelpers.BuildDirectionSegment(DirectionType.Reverse, 4)
});
StitcherTestHelpers.VerifyDirectionType(expectedDirections, mergedRead.CigarDirections.Expand().ToArray());
}
