public void GetAlignmentSet() { var reads = new List <Read>(); reads.Add(CreateRead("chr1", "ACGT", 1, "read1")); reads.Add(CreateRead("chr1", "ACGT", 1, "read2")); reads.Add(CreateRead("chr1", "ACGT", 1, "read1_mate")); reads.Add(CreateRead("chr1", "ACGT", 1, "read3_unmapped", isMapped: false, isProperPair: false)); reads.Add(CreateRead("chr1", "ACGT", 1, "read3_mate", isProperPair: false)); reads.Add(CreateRead("chr1", "ACGT", 1, "read2_mate")); var extractor = new MockAlignmentExtractor(reads); var mateFinder = new Mock <IAlignmentMateFinder>(); mateFinder.Setup(f => f.GetMate(It.IsAny <Read>())).Returns( (Read r) => r.Name.EndsWith("_mate") ? reads.FirstOrDefault(o => o.Name == r.Name.Replace("_mate", string.Empty)) : null); var stitcher = new Mock <IAlignmentStitcher>(); stitcher.Setup(s => s.TryStitch(It.IsAny <AlignmentSet>())).Callback((AlignmentSet s) => s.IsStitched = true); var config = new AlignmentSourceConfig { MinimumMapQuality = 10, OnlyUseProperPairs = false }; var source = new AlignmentSource(extractor, mateFinder.Object, stitcher.Object, config); AlignmentSet set; var numSets = 0; while ((set = source.GetNextAlignmentSet()) != null) { numSets++; if (!set.IsFullPair) { Assert.True(set.PartnerRead1.Name.Equals("read3_mate")); Assert.True(set.PartnerRead2 == null); Assert.False(set.IsStitched); } else { Assert.True(set.PartnerRead2.Name.Equals(set.PartnerRead1.Name + "_mate")); Assert.True(set.IsStitched); } } Assert.Equal(numSets, 3); }
private void ExecuteTest_ProcessReadsSeparately(bool doMate, bool doStitch) { var read = CreateRead("chr1", "ACGT", 1, "read1"); var readMate = CreateRead("chr1", "ACGT", 10, "read1mate"); var extractor = new MockAlignmentExtractor(new List <Read>() { read }); var mateFinder = new Mock <IAlignmentMateFinder>(); mateFinder.Setup(f => f.GetMate(It.IsAny <Read>())).Returns(readMate); var stitcher = new Mock <IAlignmentStitcher>(); var config = new AlignmentSourceConfig { MinimumMapQuality = 10, OnlyUseProperPairs = false }; var source = new AlignmentSource(extractor, doMate ? mateFinder.Object : null, doStitch ? stitcher.Object : null, config); var alignmentSet = source.GetNextAlignmentSet(); // verify stitching relies on pairing stitcher.Verify(s => s.TryStitch(It.IsAny <AlignmentSet>()), Times.Never); if (!doMate) { TestHelper.CompareReads(read, alignmentSet.PartnerRead1); Assert.Equal(null, alignmentSet.PartnerRead2); Assert.Equal(1, alignmentSet.ReadsForProcessing.Count); TestHelper.CompareReads(read, alignmentSet.ReadsForProcessing.First()); } else { TestHelper.CompareReads(read, alignmentSet.PartnerRead1); TestHelper.CompareReads(readMate, alignmentSet.PartnerRead2); Assert.Equal(2, alignmentSet.ReadsForProcessing.Count); TestHelper.CompareReads(read, alignmentSet.ReadsForProcessing.First()); TestHelper.CompareReads(readMate, alignmentSet.ReadsForProcessing.Last()); } }
public void Filtering() { var reads = new List <Read>(); reads.Add(CreateRead("chr1", "AAA", 1, "filtered", false, true, true, false, 10)); reads.Add(CreateRead("chr1", "AAA", 1, "filtered", true, false, true, false, 10)); reads.Add(CreateRead("chr1", "AAA", 1, "filtered_properpair", true, true, false, false, 10)); reads.Add(CreateRead("chr1", "AAA", 1, "filtered", true, true, true, true, 10)); reads.Add(CreateRead("chr1", "AAA", 1, "filtered_quality", true, true, true, false, 9)); reads.Add(CreateRead("chr1", "AAA", 1, "Filtered_CigarData", true, true, true, false, 10, false)); reads.Add(CreateRead("chr1", "AAA", 1, "yay", true, true, true, false, 10)); var extractor = new MockAlignmentExtractor(reads); var config = new AlignmentSourceConfig { MinimumMapQuality = 10, OnlyUseProperPairs = true }; var source = new AlignmentSource(extractor, null, null, config); AlignmentSet set; var fetchedCount = 0; while ((set = source.GetNextAlignmentSet()) != null) { fetchedCount++; Assert.Equal(set.PartnerRead1.Name, "yay"); } Assert.Equal(1, fetchedCount); // ------------------------- // turn off proper pairs config.OnlyUseProperPairs = false; fetchedCount = 0; extractor.Reset(); source = new AlignmentSource(extractor, null, null, config); while ((set = source.GetNextAlignmentSet()) != null) { fetchedCount++; Assert.Equal(set.PartnerRead1.Name, fetchedCount == 1 ? "filtered_properpair" : "yay"); } Assert.Equal(fetchedCount, 2); // ------------------------- // change quality cut off config.OnlyUseProperPairs = true; config.MinimumMapQuality = 9; fetchedCount = 0; extractor.Reset(); source = new AlignmentSource(extractor, null, null, config); while ((set = source.GetNextAlignmentSet()) != null) { fetchedCount++; Assert.Equal(set.PartnerRead1.Name, fetchedCount == 1 ? "filtered_quality" : "yay"); } Assert.Equal(fetchedCount, 2); }