public void GetMate()
{
var finder = new AlignmentMateFinder(1001);
var read1 = CreateAlignment(100, 500, "1");
var read1Mate = CreateAlignment(500, 100, "1");
var read2 = CreateAlignment(200, 500, "2");
var read2Mate = CreateAlignment(500, 200, "2");
var read3 = CreateAlignment(201, 600, "3");
var read3Mate = CreateAlignment(600, 201, "3");
var read4 = CreateAlignment(1000, 2001, "4");
var read4Mate = CreateAlignment(2001, 1000, "4");
var read5 = CreateAlignment(2500, 3502, "5");
var read5Mate = CreateAlignment(3502, 2500, "5");
Assert.Equal(finder.GetMate(read1), null);
Assert.Equal(finder.GetMate(read2), null);
Assert.Equal(finder.GetMate(read3), null);
TestHelper.CompareReads(finder.GetMate(read2Mate), read2);
TestHelper.CompareReads(finder.GetMate(read1Mate), read1);
TestHelper.CompareReads(finder.GetMate(read3Mate), read3);
Assert.Equal(finder.GetMate(read4), null);
TestHelper.CompareReads(finder.GetMate(read4Mate), read4);
Assert.Equal(finder.GetMate(read5), null);
// jg - turned this behavior off for now because it's really inefficient
// Assert.Throws<Exception>(() => finder.GetMate(read5Mate)); // out of window
Assert.Throws <ArgumentException>(() => finder.GetMate(CreateAlignment(2500, 2500, null))); // null name
Assert.Throws <ArgumentException>(() => finder.GetMate(CreateAlignment(2500, 2500, ""))); // empty name
Assert.Throws <ArgumentException>(() => finder.GetMate(CreateAlignment(2500, -1, null))); // invalid mate position
}
public void GetMate()
{
var finder = new AlignmentMateFinder();
var read1 = CreateAlignment(100, 500, "1");
var read1Mate = CreateAlignment(500, 100, "1");
var read2 = CreateAlignment(200, 400, "2");
var read2Mate = CreateAlignment(400, 200, "2");
var read3 = CreateAlignment(201, 600, "3");
var read3Mate = CreateAlignment(600, 201, "3");
var read4 = CreateAlignment(1000, 2000, "4");
var read4Mate = CreateAlignment(2000, 1000, "4");
var read5 = CreateAlignment(2500, 3501, "5");
var read5Mate = CreateAlignment(3501, 2500, "5");
Assert.Equal(finder.LastClearedPosition, null);
Assert.Equal(finder.NextMatePosition, null);
Assert.Equal(finder.GetMate(read1), null);
Assert.Equal(finder.LastClearedPosition, 99);
Assert.Equal(finder.NextMatePosition, 500);
Assert.Equal(finder.GetMate(read2), null);
Assert.Equal(finder.LastClearedPosition, 99);
Assert.Equal(finder.NextMatePosition, 400);
Assert.Equal(finder.GetMate(read3), null);
Assert.Equal(finder.LastClearedPosition, 99);
ReadTests.CompareReads(finder.GetMate(read2Mate), read2);
Assert.Equal(finder.LastClearedPosition, 99);
Assert.Equal(finder.NextMatePosition, 500);
ReadTests.CompareReads(finder.GetMate(read1Mate), read1);
Assert.Equal(finder.LastClearedPosition, 200);
Assert.Equal(finder.NextMatePosition, 600);
ReadTests.CompareReads(finder.GetMate(read3Mate), read3);
Assert.Equal(finder.LastClearedPosition, null);
Assert.Equal(finder.GetMate(read4), null);
Assert.Equal(finder.LastClearedPosition, 999);
ReadTests.CompareReads(finder.GetMate(read4Mate), read4);
Assert.Equal(finder.LastClearedPosition, null);
Assert.Equal(finder.GetMate(read5), null);
Assert.Equal(finder.LastClearedPosition, 2499);
Assert.Equal(finder.GetMate(read5Mate), null); // out of window gets tossed
Assert.Equal(finder.LastClearedPosition, null);
Assert.Equal(finder.NextMatePosition, null);
Assert.Equal(2, finder.ReadsUnpairable);
Assert.Throws<ArgumentException>(() => finder.GetMate(CreateAlignment(2500, 2500, null))); // null name
Assert.Throws<ArgumentException>(() => finder.GetMate(CreateAlignment(2500, 2500, ""))); // empty name
Assert.Throws<ArgumentException>(() => finder.GetMate(CreateAlignment(2500, -1, null))); // invalid mate position
}
public void GetUnpaired()
{
var finder = new AlignmentMateFinder();
var read1 = CreateAlignment(100, 500, "1");
Assert.Null(finder.GetMate(read1));
Assert.Equal(new[] {read1.Name}, finder.GetUnpairedReads().Select(x => x.Name).ToArray());
}
public static ISomaticVariantCaller CreateMockVariantCaller(VcfFileWriter vcfWriter, ApplicationOptions options, ChrReference chrRef, MockAlignmentExtractor mockAlignmentExtractor, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null)
{
var config = new AlignmentSourceConfig
{
MinimumMapQuality = options.MinimumMapQuality,
OnlyUseProperPairs = options.OnlyUseProperPairs,
};
//var mateFinder = options.StitchReads ? new AlignmentMateFinder() : null;
AlignmentMateFinder mateFinder = null;
var alignmentSource = new AlignmentSource(mockAlignmentExtractor, mateFinder, config);
var variantFinder = new CandidateVariantFinder(options.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var coverageCalculator = new CoverageCalculator();
var alleleCaller = new AlleleCaller(new VariantCallerConfig
{
IncludeReferenceCalls = options.OutputgVCFFiles,
MinVariantQscore = options.MinimumVariantQScore,
MaxVariantQscore = options.MaximumVariantQScore,
VariantQscoreFilterThreshold = options.FilteredVariantQScore > options.MinimumVariantQScore ? options.FilteredVariantQScore : (int?)null,
MinCoverage = options.MinimumDepth,
MinFrequency = options.MinimumFrequency,
EstimatedBaseCallQuality = options.AppliedNoiseLevel == -1 ? options.MinimumBaseCallQuality : options.AppliedNoiseLevel,
StrandBiasModel = options.StrandBiasModel,
StrandBiasFilterThreshold = options.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = options.FilterOutVariantsPresentOnlyOneStrand,
ChrReference = chrRef
},
coverageCalculator: coverageCalculator,
variantCollapser: options.Collapse ? new VariantCollapser(null, coverageCalculator) : null);
var stateManager = new RegionStateManager(
expectStitchedReads: mockAlignmentExtractor.SourceIsStitched,
trackOpenEnded: options.Collapse, trackReadSummaries: options.CoverageMethod == CoverageMethod.Approximate);
//statmanager is an allele source
Assert.Equal(0, stateManager.GetAlleleCount(1, AlleleType.A, DirectionType.Forward));
return(new SomaticVariantCaller(
alignmentSource,
variantFinder,
alleleCaller,
vcfWriter,
stateManager,
chrRef,
null,
biasFileWriter));
}
public void ReadPurgedEventTriggered()
{
var finder = new AlignmentMateFinder(maxWindow:500);
Read purgedRead = null;
finder.ReadPurged += read => purgedRead = read;
// reads whose mates will never be encountered because they are before the current position
var read1 = CreateAlignment(5000, 100, "1");
Assert.Equal(finder.GetMate(read1), null);
Assert.Equal(read1.Name, purgedRead.Name);
// reads whose mates are more than the max distance before a read being added (and thus will not be encountered)
var read2 = CreateAlignment(5000, 5100, "2");
Assert.Equal(finder.GetMate(read2), null);
Assert.Equal(finder.GetMate(CreateAlignment(6000, 6100, "3")), null);
Assert.Equal(read2.Name, purgedRead.Name);
}
public void BadPairs()
{
var finder = new AlignmentMateFinder();
// mismatch on mate positions
var read6 = CreateAlignment(2500, 2600, "6");
var read6Mate = CreateAlignment(2600, 2501, "6");
var read7 = CreateAlignment(2500, 2601, "7");
var read7Mate = CreateAlignment(2602, 2500, "7");
Assert.Equal(finder.GetMate(read6), null);
Assert.Equal(finder.LastClearedPosition, 2499);
Assert.Equal(finder.GetMate(read6Mate), null);
Assert.Equal(finder.LastClearedPosition, null); // both cleared out
Assert.Equal(finder.GetMate(read7), null);
Assert.Equal(finder.LastClearedPosition, 2499);
Assert.Equal(finder.GetMate(read7Mate), null);
Assert.Equal(finder.LastClearedPosition, null); // both cleared out
}
protected virtual IAlignmentSource CreateAlignmentSource(ChrReference chrReference, string bamFilePath, List <string> chrsToProcess = null)
{
AlignmentMateFinder mateFinder = null;
var alignmentExtractor = new BamFileAlignmentExtractor(bamFilePath, chrReference.Name, _bamIntervalLookup.ContainsKey(bamFilePath) && _options.SkipNonIntervalAlignments ? _bamIntervalLookup[bamFilePath] : null);
//Warn if the bam has sequences ordered differently to the reference genome.
//That would confuse us because we will not know how the user wants to order the output gvcf.
if (alignmentExtractor.SequenceOrderingIsNotConsistent(chrsToProcess))
{
Logger.WriteToLog("Warning: Reference sequences in the bam do not match the order of the reference sequences in the genome. Check bam " + bamFilePath);
Logger.WriteToLog("Variants will be ordered according to the reference genome");
}
var config = new AlignmentSourceConfig
{
MinimumMapQuality = _options.MinimumMapQuality,
OnlyUseProperPairs = _options.OnlyUseProperPairs,
};
return(new AlignmentSource(alignmentExtractor, mateFinder, config));
}
protected virtual IAlignmentSource CreateAlignmentSource(ChrReference chrReference, string bamFilePath, bool commandLineSaysStitched, List <string> chrsToProcess = null)
{
AlignmentMateFinder mateFinder = null;
var alignmentExtractor = new BamFileAlignmentExtractor(bamFilePath, commandLineSaysStitched, chrReference.Name);
//Warn if the bam has sequences ordered differently to the reference genome.
//That would confuse us because we will not know how the user wants to order the output gvcf.
if (alignmentExtractor.SequenceOrderingIsNotConsistent(chrsToProcess))
{
Logger.WriteToLog("Warning: Reference sequences in the bam do not match the order of the reference sequences in the genome. Check bam " + bamFilePath);
Logger.WriteToLog("Variants will be ordered according to the reference genome");
}
var config = new AlignmentSourceConfig
{
MinimumMapQuality = _options.BamFilterParameters.MinimumMapQuality,
OnlyUseProperPairs = _options.BamFilterParameters.OnlyUseProperPairs,
SkipDuplicates = _options.BamFilterParameters.RemoveDuplicates
};
return(new AlignmentSource(alignmentExtractor, mateFinder, config));
}
