private PhasedVcfWriter InitializeWriter(bool crushVcf)
{
if (File.Exists(_outputFile))
{
File.Delete(_outputFile);
}
var writerConfig = new VcfWriterConfig();
writerConfig.AllowMultipleVcfLinesPerLoci = (!crushVcf);
writerConfig.ShouldOutputStrandBiasAndNoiseLevel = true;
writerConfig.ShouldOutputNoCallFraction = true;
writerConfig.MinFrequencyThreshold = 0.01f;
var writer = new PhasedVcfWriter(_outputFile, writerConfig, new VcfWriterInputContext(), _origHeader, "tester command line");
return(writer);
}
public void WriteANbhd()
{
var outputFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "PhasedVcfFileNbhdWriterTest.vcf");
var inputFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "MergerInput.vcf");
var expectedFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "MergerOutput.vcf");
File.Delete(outputFilePath);
var context = new VcfWriterInputContext
{
QuotedCommandLineString = "myCommandLine",
SampleName = "mySample",
ReferenceName = "myReference",
ContigsByChr = new List <Tuple <string, long> >
{
new Tuple <string, long>("chr1", 10001),
new Tuple <string, long>("chrX", 500)
}
};
var config = new VcfWriterConfig
{
DepthFilterThreshold = 500,
VariantQualityFilterThreshold = 30,
FrequencyFilterThreshold = 0.007f,
ShouldOutputNoCallFraction = true,
ShouldOutputStrandBiasAndNoiseLevel = true,
EstimatedBaseCallQuality = 23,
PloidyModel = PloidyModel.Somatic,
AllowMultipleVcfLinesPerLoci = true
};
var writer = new PhasedVcfWriter(outputFilePath, config, new VcfWriterInputContext(), new List <string>()
{
}, null);
var reader = new VcfReader(inputFilePath, true);
//set up the original variants
var originalVcfVariant1 = TestHelper.CreateDummyAllele("chr2", 116380048, "A", "New", 1000, 156);
var originalVcfVariant2 = TestHelper.CreateDummyAllele("chr2", 116380048, "AAA", "New", 1000, 156);
var originalVcfVariant4 = TestHelper.CreateDummyAllele("chr7", 116380051, "A", "New", 1000, 156);
var originalVcfVariant5 = TestHelper.CreateDummyAllele("chr7", 116380052, "AC", "New", 1000, 156);
var vs1 = new VariantSite((originalVcfVariant1));
var vs2 = new VariantSite((originalVcfVariant2));
var vs4 = new VariantSite((originalVcfVariant4));
var vs5 = new VariantSite((originalVcfVariant5));
//have to replace variants at positon 116380048 (we call two new MNVS here)
var nbhd1 = new VcfNeighborhood(new VariantCallingParameters(), 0, "chr2", vs1, vs2, "");
nbhd1.SetRangeOfInterest();
//have to replace variants at positon 116380051 and 52 (we call one new MNV at 51)
var nbhd2 = new VcfNeighborhood(new VariantCallingParameters(), 0, "chr7", vs4, vs5, "");
nbhd2.SetRangeOfInterest();
VcfMerger merger = new VcfMerger(reader);
List <CalledAllele> allelesPastNbh = new List <CalledAllele>();
nbhd1.CalledVariants = new Dictionary <int, List <CalledAllele> > {
{ originalVcfVariant1.ReferencePosition, new List <CalledAllele> {
originalVcfVariant1, originalVcfVariant2
} }
};
nbhd2.CalledVariants = new Dictionary <int, List <CalledAllele> > {
{ originalVcfVariant4.ReferencePosition, new List <CalledAllele> {
originalVcfVariant4
} }
};
allelesPastNbh = merger.WriteVariantsUptoChr(writer, allelesPastNbh, nbhd1.ReferenceName);
allelesPastNbh = merger.WriteVariantsUptoIncludingNbhd(nbhd1, writer, allelesPastNbh);
allelesPastNbh = merger.WriteVariantsUptoChr(writer, allelesPastNbh, nbhd2.ReferenceName);
allelesPastNbh = merger.WriteVariantsUptoIncludingNbhd(nbhd2, writer, allelesPastNbh);
merger.WriteRemainingVariants(writer, allelesPastNbh);
writer.Dispose();
var expectedLines = File.ReadLines(expectedFilePath).ToList();
var outputLines = File.ReadLines(outputFilePath).ToList();
Assert.Equal(expectedLines.Count(), outputLines.Count());
for (int i = 0; i < expectedLines.Count; i++)
{
Assert.Equal(expectedLines[i], outputLines[i]);
}
}
public void FilterHeader()
{
var outputFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "PhasedVcfFileWriterTests.vcf");
File.Delete(outputFilePath);
var context = new VcfWriterInputContext
{
QuotedCommandLineString = "myCommandLine",
SampleName = "mySample",
ReferenceName = "myReference",
ContigsByChr = new List <Tuple <string, long> >
{
new Tuple <string, long>("chr1", 10001),
new Tuple <string, long>("chrX", 500)
}
};
// Variant strand bias too high or coverage on only one strand
var config = new VcfWriterConfig
{
DepthFilterThreshold = 500,
VariantQualityFilterThreshold = 30,
FrequencyFilterThreshold = 0.007f,
ShouldOutputNoCallFraction = true,
ShouldOutputStrandBiasAndNoiseLevel = true,
EstimatedBaseCallQuality = 23,
PloidyModel = PloidyModel.Diploid,
};
//note, scylla has no SB or RMxN or R8 filters.
var variants = new List <CalledAllele>
{
TestHelper.CreateDummyAllele("chrX", 123, "A", "C", 1000, 156),
TestHelper.CreateDummyAllele("chr10", 124, "A", "C", 1000, 156),
};
var originalHeader = new List <string>
{
"##fileformat=VCFv4.1",
"##fileDate=20160620",
"##source=Pisces 1.0.0.0",
"##Pisces_cmdline=\"-B KRAS_42_S1.bam -g -MinimumFrequency 0.01 -MinBaseCallQuality 21 -MaxVariantQScore 100 -MinCoverage 300 -MaxAcceptableStrandBiasFilter 0.5 -MinVariantQScore 20 -VariantQualityFilter 20 -gVCF true -CallMNVs True -out \\myout",
"##reference=WholeGenomeFASTA",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">",
"##FILTER=<ID=q20,Description=\"Quality score less than 20\">",
"##FILTER=<ID=SB,Description=\"Variant strand bias too high\">",
"##FILTER=<ID=R5x9,Description=\"Repeats of part or all of the variant allele (max repeat length 5) in the reference greater than or equal to 9\">",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">",
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HD700n560_miseq1_S7.bam"
};
var writer = new PhasedVcfWriter(outputFilePath, config, new VcfWriterInputContext(), originalHeader, null);
writer.WriteHeader();
writer.Write(variants);
writer.Dispose();
VcfReader reader = new VcfReader(outputFilePath);
List <string> writtenHeader = reader.HeaderLines;
reader.Dispose();
var expectedHeader1 = new List <string>
{
"##fileformat=VCFv4.1",
"##fileDate=20160620",
"##source=Pisces 1.0.0.0",
"##Pisces_cmdline=\"-B KRAS_42_S1.bam -g -MinimumFrequency 0.01 -MinBaseCallQuality 21 -MaxVariantQScore 100 -MinCoverage 300 -MaxAcceptableStrandBiasFilter 0.5 -MinVariantQScore 20 -VariantQualityFilter 20 -gVCF true -CallMNVs True -out \\myout",
"##VariantPhaser=Scylla 1.0.0.0",
"##reference=WholeGenomeFASTA",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">",
"##FILTER=<ID=q20,Description=\"Quality score less than 20\">",
"##FILTER=<ID=SB,Description=\"Variant strand bias too high\">",
"##FILTER=<ID=R5x9,Description=\"Repeats of part or all of the variant allele (max repeat length 5) in the reference greater than or equal to 9\">",
"##FILTER=<ID=q30,Description=\"Quality score less than 30, by Scylla\">",
"##FILTER=<ID=LowDP,Description=\"Low coverage (DP tag), therefore no genotype called, by Scylla\">",
"##FILTER=<ID=LowVariantFreq,Description=\"Variant frequency less than 0.0070, by Scylla\">",
"##FILTER=<ID=MultiAllelicSite,Description=\"Variant does not conform to diploid model, by Scylla\">",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">",
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HD700n560_miseq1_S7.bam"
};
Assert.Equal(expectedHeader1.Count, writtenHeader.Count);
for (int i = 0; i < expectedHeader1.Count; i++)
{
//let version numbers differ
if (expectedHeader1[i].StartsWith("##VariantPhaser=Scylla"))
{
Assert.True(writtenHeader[i].StartsWith("##VariantPhaser=Scylla"));
continue;
}
Assert.Equal(expectedHeader1[i], writtenHeader[i]);
}
config = new VcfWriterConfig
{
DepthFilterThreshold = 500,
VariantQualityFilterThreshold = 22,
FrequencyFilterThreshold = 0.007f,
EstimatedBaseCallQuality = 23,
PloidyModel = PloidyModel.Somatic,
};
originalHeader = new List <string>
{
"##fileformat=VCFv4.1",
"##fileDate=20160620",
"##source=Pisces 1.0.0.0",
"##Pisces_cmdline=\"-B KRAS_42_S1.bam -g -MinimumFrequency 0.01 -MinBaseCallQuality 21 -MaxVariantQScore 100 -MinCoverage 300 -MaxAcceptableStrandBiasFilter 0.5 -MinVariantQScore 20 -VariantQualityFilter 20 -gVCF true -CallMNVs True -out \\myout",
"##reference=WholeGenomeFASTA",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">",
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HD700n560_miseq1_S7.bam"
};
writer = new PhasedVcfWriter(outputFilePath, config, new VcfWriterInputContext(), originalHeader, null);
var expectedHeader2 = new List <string>
{
"##fileformat=VCFv4.1",
"##fileDate=20160620",
"##source=Pisces 1.0.0.0",
"##Pisces_cmdline=\"-B KRAS_42_S1.bam -g -MinimumFrequency 0.01 -MinBaseCallQuality 21 -MaxVariantQScore 100 -MinCoverage 300 -MaxAcceptableStrandBiasFilter 0.5 -MinVariantQScore 20 -VariantQualityFilter 20 -gVCF true -CallMNVs True -out \\myout",
"##VariantPhaser=Scylla 1.0.0.0",
"##reference=WholeGenomeFASTA",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">",
"##FILTER=<ID=q22,Description=\"Quality score less than 22, by Scylla\">",
"##FILTER=<ID=LowDP,Description=\"Low coverage (DP tag), therefore no genotype called, by Scylla\">",
"##FILTER=<ID=LowVariantFreq,Description=\"Variant frequency less than 0.0070, by Scylla\">",
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HD700n560_miseq1_S7.bam"
};
writer.WriteHeader();
writer.Write(variants);
writer.Dispose();
reader = new VcfReader(outputFilePath);
writtenHeader = reader.HeaderLines;
reader.Dispose();
Assert.Equal(expectedHeader2.Count, writtenHeader.Count);
for (int i = 0; i < expectedHeader2.Count; i++)
{
//let version numbers differ
if (expectedHeader1[i].StartsWith("##VariantPhaser=Scylla"))
{
Assert.True(writtenHeader[i].StartsWith("##VariantPhaser=Scylla"));
continue;
}
Assert.Equal(expectedHeader2[i], writtenHeader[i]);
}
}
public void WriteADiploidNbhd()
{
var outputDir = Path.Combine(TestPaths.LocalScratchDirectory, "MergerWriteADiploidNbhd");
var outputFilePath = Path.Combine(outputDir, "TinyDiploid.Phased.vcf");
var inputFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "TinyDiploid.vcf");
var expectedFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "TinyDiploidOutput.vcf");
TestHelper.RecreateDirectory(outputDir);
var context = new VcfWriterInputContext
{
QuotedCommandLineString = "myCommandLine",
SampleName = "mySample",
ReferenceName = "myReference",
ContigsByChr = new List <Tuple <string, long> >
{
new Tuple <string, long>("chr1", 10001),
new Tuple <string, long>("chr22", 51304566),
new Tuple <string, long>("chrX", 500)
}
};
var config = new VcfWriterConfig
{
DepthFilterThreshold = 500,
VariantQualityFilterThreshold = 30,
FrequencyFilterThreshold = 0.007f,
ShouldOutputNoCallFraction = true,
ShouldOutputStrandBiasAndNoiseLevel = true,
EstimatedBaseCallQuality = 23,
PloidyModel = PloidyModel.DiploidByThresholding,
AllowMultipleVcfLinesPerLoci = false
};
var writer = new PhasedVcfWriter(outputFilePath, config, new VcfWriterInputContext(), new List <string>()
{
}, null);
var reader = new AlleleReader(inputFilePath, true);
//set up the original variants
var originalVcfVariant1 = TestHelper.CreateDummyAllele("chr1", 1, "A", "G", 1000, 156);
var originalVcfVariant2 = TestHelper.CreateDummyAllele("chr1", 1, "A", "T", 1000, 156);
var originalVcfVariant4 = TestHelper.CreateDummyAllele("chr22", 1230237, "GTC", "G", 1000, 156);
var originalVcfVariant5 = TestHelper.CreateDummyAllele("chr22", 1230237, "GTC", "GTCT", 1000, 156);
var vs1 = new VariantSite((originalVcfVariant1));
var vs2 = new VariantSite((originalVcfVariant2));
var vs4 = new VariantSite((originalVcfVariant4));
var vs5 = new VariantSite((originalVcfVariant5));
//have to replace variants at positon 116380048 (we call two new MNVS here)
var nbhd1 = new VcfNeighborhood(0, "chr1", vs1, vs2);
var calledNbh1 = new CallableNeighborhood(nbhd1, new VariantCallingParameters());
VcfMerger merger = new VcfMerger(reader);
List <Tuple <CalledAllele, string> > alleleTuplesPastNbhd = new List <Tuple <CalledAllele, string> >();
//we will just say, we called the variants that were in the origina vcf. Ie, we agree with it.
calledNbh1.CalledVariants = new Dictionary <int, List <CalledAllele> > {
{ originalVcfVariant1.ReferencePosition, new List <CalledAllele> {
originalVcfVariant1, originalVcfVariant2
} }
};
//Realizes the first nbhd starts at chr1 . We have to do something with the first lines of the vcf (chr1 1 . A G,T)
//so, alleleTuplesPastNbhd = chr1 1 . A G,T
alleleTuplesPastNbhd = merger.WriteVariantsUptoChr(writer, alleleTuplesPastNbhd, nbhd1.ReferenceName);
Assert.True(alleleTuplesPastNbhd[0].Item1.IsSameAllele(originalVcfVariant1));
Assert.True(alleleTuplesPastNbhd[1].Item1.IsSameAllele(originalVcfVariant2));
//This method writes everything up to the end of nbhd 1,
//so "(chr1 1 . A G,T)" from the vcf and the variants scylla detected "(chr1 1 . A G,T)" need to be dealt with.
//Since these 4 variants are actually the same two, we need to remove the vcf ones and only write the scylla ones.
//Thn we peek into the vcf and see the next line is "chr22 1230237 . GTC G,GTCT", clearly outside nbh1.
//so we write out everything we need for nbhd1, and save the peeked line
alleleTuplesPastNbhd = merger.WriteVariantsUptoIncludingNbhd(writer, alleleTuplesPastNbhd, calledNbh1);
Assert.True(alleleTuplesPastNbhd[0].Item1.IsSameAllele(originalVcfVariant4));
Assert.True(alleleTuplesPastNbhd[1].Item1.IsSameAllele(originalVcfVariant5));
//now write out
//chr22 1230237.GTC G,GTCT 50 DP = 1370 GT: GQ: AD: DP: VF: NL: SB: NC: US 1 / 2:100:185,68:364:0.258:20:-100.0000:0.0000:0,0,0,0,0,0,1,1,0,0,0,2
//chrX 79.CG GTG,AA 50 DP = 1370 GT: GQ: AD: DP: VF: NL: SB: NC: US 1 / 2:100:185,68:364:0.258:20:-100.0000:0.0000:0,0,0,0,0,0,1,1,0,0,0,2
merger.WriteRemainingVariants(writer, alleleTuplesPastNbhd);
writer.Dispose();
var expectedLines = File.ReadLines(expectedFilePath).ToList();
var outputLines = File.ReadLines(outputFilePath).ToList();
Assert.Equal(expectedLines.Count(), outputLines.Count());
for (int i = 0; i < expectedLines.Count; i++)
{
Assert.Equal(expectedLines[i], outputLines[i]);
}
}
