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);
;
// -----------------------------------------------
// 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);
stitcher.TryStitch(alignmentSet);
Assert.Equal(2, alignmentSet.ReadsForProcessing.Count);
StitcherTestHelpers.TestUnstitchableReads(read1, read2_noOverlap, 0, (unStitchableReads) =>
{
Assert.Equal(1, unStitchableReads.Count(x => StitcherTestHelpers.VerifyReadsEqual(read1, x)));
Assert.Equal(1, unStitchableReads.Count(x => StitcherTestHelpers.VerifyReadsEqual(read2_noOverlap, x)));
});
// -----------------------------------------------
// No overlap, reads are directly neighboring
// -----------------------------------------------
// Shouldn't stitch
alignmentSet = new AlignmentSet(read1, read2_nonOverlap_border);
stitcher.TryStitch(alignmentSet);
Assert.Equal(2, alignmentSet.ReadsForProcessing.Count);
StitcherTestHelpers.TestUnstitchableReads(read1, read2_nonOverlap_border, 0, (unStitchableReads) =>
{
Assert.Equal(1, unStitchableReads.Count(x => StitcherTestHelpers.VerifyReadsEqual(read1, x)));
Assert.Equal(1, unStitchableReads.Count(x => StitcherTestHelpers.VerifyReadsEqual(read2_nonOverlap_border, x)));
});
// -----------------------------------------------
// 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 void CallSomaticVariants_MergeReadsWithInsertion_BoundaryTests()
{
//Migrated from old Pisces: Originally called CallSomaticVariants_MergeReadsWithInsertion_BoundaryTests
// insertion at edge of read
//0 1 2 3 - - - 4 5 6 7 8 9
//- C A T A T A G G
//- - - - A T A G G T A A
var read1 = TestHelper.CreateRead("chr1",
"CATATAGG",
1,
new CigarAlignment("3M3I2M"),
new byte[8],
4);
var read2 = TestHelper.CreateRead("chr1",
"ATAGGTAA",
4,
new CigarAlignment("3S5M"),
new byte[8],
1);
TestSuccesfullyStitchedRead(read1, read2, 0, "3M3I5M", (mergedRead) =>
{
Assert.NotNull(mergedRead);
Assert.Equal(mergedRead.Sequence, "CATATAGGTAA");
});
//0 1 2 3 - - - 4 5 6 7 8 9
//- C A T A T A G G
//- - - - - T A G G T A A
read1 = TestHelper.CreateRead("chr1", "CATATAGG", 1, new CigarAlignment("3M3I2M"),
new byte[8], 4);
read2 = TestHelper.CreateRead("chr1", "TAGGTAA", 4, new CigarAlignment("2S5M"),
new byte[8], 1);
TestSuccesfullyStitchedRead(read1, read2, 0, "3M3I5M", (mergedRead) =>
{
Assert.NotNull(mergedRead);
Assert.Equal(mergedRead.Sequence, "CATATAGGTAA");
});
// shouldnt be able to stitch soft clipped areas only if XC tag not provided
//0 1 2 3 - - - 4 5 6 7 8 9
//- C A T A T A G G
//- - - - - T A G G T A A
read1 = TestHelper.CreateRead("chr1", "CATATAGG", 1, new CigarAlignment("3M5S"),
new byte[8], 4);
read2 = TestHelper.CreateRead("chr1", "TAGGTAA", 4, new CigarAlignment("2S5M"),
new byte[8], 1);
StitcherTestHelpers.TestUnstitchableReads(read1, read2, 0, (unStitchableReads) =>
{
Assert.Equal(1, unStitchableReads.Count(x => StitcherTestHelpers.VerifyReadsEqual(read1, x)));
Assert.Equal(1, unStitchableReads.Count(x => StitcherTestHelpers.VerifyReadsEqual(read2, x)));
});
}
