public void VennVcf_EmptyInputTest()
{
var outDir = TestPaths.LocalTestDataDirectory;
var VcfPathRoot = _TestDataPath;
string VcfA = Path.Combine(VcfPathRoot, "Empty_S1.vcf");
string VcfB = Path.Combine(VcfPathRoot, "Empty_S2.vcf");
string OutputPath = Path.Combine(outDir, "EmptyConsensus.vcf");
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = Path.Combine(outDir, "EmptyConsensus.vcf");
parameters.OutputDirectory = outDir;
parameters.DebugMode = true;
VennProcessor Venn = new VennProcessor(new string[] { VcfA, VcfB }, parameters);
Venn.DoPairwiseVenn(false);
Assert.True(File.Exists(OutputPath));
var observedVariants = VcfReader.GetAllVariantsInFile(OutputPath);
Assert.Equal(0, observedVariants.Count);
}
public void VennVcf_GtTest()
{
var outDir = TestPaths.LocalScratchDirectory;
var VcfPathRoot = _TestDataPath;
string VcfA = Path.Combine(VcfPathRoot, "gtTests_S15.vcf");
string VcfB = Path.Combine(VcfPathRoot, "gtTests_S18.vcf");
string OutputPath = Path.Combine(outDir, "gtConsensusOut.vcf");
string ExpectedPath = Path.Combine(VcfPathRoot, "gtConsensus.vcf");
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = OutputPath;
parameters.OutputDirectory = outDir;
VennProcessor Venn = new VennProcessor(new string[] { VcfA, VcfB }, parameters);
Venn.DoPairwiseVenn(false);
Assert.True(File.Exists(OutputPath));
var expectedVariants = VcfReader.GetAllVariantsInFile(ExpectedPath);
var observedVariants = VcfReader.GetAllVariantsInFile(OutputPath);
Assert.Equal(expectedVariants.Count, observedVariants.Count);
for (int i = 0; i < expectedVariants.Count; i++)
{
var ExpectedVariant = expectedVariants[i];
var OutputVariant = observedVariants[i];
Assert.Equal(ExpectedVariant.ToString(), OutputVariant.ToString());
}
}
public void CallSomaticVariants_LowDepthTest()
{
List <ChrReference> chrRef = new List <ChrReference>()
{
new ChrReference()
{
Name = "chr19",
Sequence = "TTGTCAGTGCGCTTTTCCCAACACCACCTGCTCCGACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGGCGAAAAAAAAAAAAAAAAAAAAAAAAAA"
}
};
var options = new ApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
//IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
MaxSizeMNV = 100,
OutputgVCFFiles = true,
MinimumCoverage = 1000,
OutputFolder = UnitTestPaths.TestDataDirectory
};
var vcfFilePath = Path.ChangeExtension(options.BAMPaths[0], "genome.vcf");
var factory = new Factory(options);
IGenome genomeRef;
genomeRef = new MockGenome(chrRef);
var bp = new BamProcessor(factory, genomeRef);
bp.Execute(1);
List <VcfVariant> coverage1000results = VcfReader.GetAllVariantsInFile(vcfFilePath);
options = new ApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
// IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
OutputgVCFFiles = true,
OutputFolder = UnitTestPaths.TestDataDirectory
};
factory = new Factory(options);
bp = new BamProcessor(factory, genomeRef);
bp.Execute(1);
List <VcfVariant> coverage10results = VcfReader.GetAllVariantsInFile(vcfFilePath);
// Assert.NotEqual(coverage1000results.Count, coverage10results.Count);
// Assert.Equal(coverage1000results.Count, 84);
// Assert.Equal(coverage10results.Count, 100);
}
private void CompareVariants(string expectedResultsFilePath, string actualResultsFilePath)
{
List <VcfVariant> results = VcfReader.GetAllVariantsInFile(actualResultsFilePath);
List <VcfVariant> expected = VcfReader.GetAllVariantsInFile(expectedResultsFilePath);
Assert.Equal(results.Count, expected.Count);
for (int i = 0; i < results.Count; i++)
{
Assert.Equal(expected[i].ToString(), results[i].ToString());
}
}
public void VennVcf_CombineTwoPoolVariants_MergeRefCalls()
{
//this is from an issue where there were multiple co-located variants in one pool,
//and just ref in the other, at chr15 92604460. The consensus answer should be
// a single ref call (and not multiple ref calls!).
var outDir = TestPaths.LocalScratchDirectory;
var vcfPathRoot = _TestDataPath;
string VcfPath_PoolA = Path.Combine(vcfPathRoot, "C64-Ct-4_S17.genome.vcf");
string VcfPath_PoolB = Path.Combine(vcfPathRoot, "C64-Ct-4_S18.genome.vcf");
string VcfPath_Consensus = Path.Combine(vcfPathRoot, "ExpectedConsensus2.vcf");
string OutputPath = Path.Combine(outDir, "Consensus2.vcf");
if (File.Exists(OutputPath))
{
File.Delete(OutputPath);
}
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.InputFiles = new string[] { VcfPath_PoolA, VcfPath_PoolB };
parameters.OutputDirectory = outDir; //Path.Combine(outDir, "RefMergeOut.vcf");
parameters.ConsensusFileName = OutputPath;
VennProcessor venn = new VennProcessor(parameters.InputFiles, parameters);
venn.DoPairwiseVenn(false);
Assert.Equal(File.Exists(OutputPath), true);
List <VcfVariant> CombinedVariants = VcfReader.GetAllVariantsInFile(OutputPath);
List <VcfVariant> ExpectedVariants = VcfReader.GetAllVariantsInFile(VcfPath_Consensus);
Assert.Equal(ExpectedVariants.Count, CombinedVariants.Count);
int NumVariantsAtPos92604460 = 0;
for (int i = 0; i < ExpectedVariants.Count; i++)
{
VcfVariant EVariant = ExpectedVariants[i];
VcfVariant Variant = CombinedVariants[i];
if ((Variant.ReferencePosition == 92604460) &&
(Variant.ReferenceName == "chr15"))
{
NumVariantsAtPos92604460++;
}
Assert.Equal(EVariant.ToString(), Variant.ToString());
}
Assert.Equal(NumVariantsAtPos92604460, 1);
}
public Dictionary <string, Dictionary <int, List <Mapping> > > IntersectVcfWithPanelVar(string file)
{
List <VcfVariant> allVariantsFromVcf = VcfReader.GetAllVariantsInFile(file);
Dictionary <string, Dictionary <int, List <Mapping> > > foundVariantDataByChrAndPos =
new Dictionary <string, Dictionary <int, List <Mapping> > >();
foundVariantDataByChrAndPos["chr12"] = new Dictionary <int, List <Mapping> >();
foundVariantDataByChrAndPos["chr1"] = new Dictionary <int, List <Mapping> >();
foreach (VcfVariant vcfVar in allVariantsFromVcf)
{
string myChr = vcfVar.ReferenceName;
int myPos = vcfVar.ReferencePosition;
if ((myChr != "chr12") && (myChr != "chr1"))
{
continue;
}
if (!TableDataByChrAndPos.ContainsKey(myChr))
{
continue;
}
//we have a Var or ref call at a position we care about
if (TableDataByChrAndPos[myChr].ContainsKey(vcfVar.ReferencePosition))
{
List <RefPanelEntry> panelEntryAtPOsition = TableDataByChrAndPos[myChr][myPos];
if (!foundVariantDataByChrAndPos[myChr].ContainsKey(myPos))
{
foundVariantDataByChrAndPos[myChr][myPos] = new List <Mapping>();
}
foreach (RefPanelEntry entry in panelEntryAtPOsition)
{
if (CheckForMatch(entry, vcfVar))
{
Mapping mapping = new Mapping();
mapping.Var = vcfVar;
mapping.Entry = entry;
foundVariantDataByChrAndPos[myChr][myPos].Add(mapping);
break;
}
}
}
}
return(foundVariantDataByChrAndPos);
}
public void GetNeighborhoodsFromMessyVCF()
{
var vcfFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "verymutated.genome.vcf");
var neighborhoodManager = CreateNbhdBuilder(_sourceVcf0);
Assert.Equal(0, neighborhoodManager.GetBatchOfNeighborhoods(0).Count());
List <VcfVariant> LotsOfCoLocatedVariants = VcfReader.GetAllVariantsInFile(vcfFilePath);
neighborhoodManager = CreateNbhdBuilder(_sourceVcf_Mutated);
var neighborhoods = neighborhoodManager.GetBatchOfNeighborhoods(0);
Assert.Equal(1, neighborhoods.Count());
Assert.Equal(12, neighborhoods.First().VcfVariantSites.Count());
}
public void GetNeighborhoodsFromMessyVCF()
{
var vcfFilePath = Path.Combine(UnitTestPaths.TestDataDirectory, "verymutated.genome.vcf");
var outFolder = Path.Combine(UnitTestPaths.TestDataDirectory, "Out");
var neighborhoodManager = CreateBuilder(new List <VcfVariant>()
{
});
Assert.Equal(0, neighborhoodManager.GetNeighborhoods().Count());
List <VcfVariant> LotsOfCoLocatedVariants = VcfReader.GetAllVariantsInFile(vcfFilePath);
neighborhoodManager = CreateBuilder(LotsOfCoLocatedVariants);
var neighborhoods = neighborhoodManager.GetNeighborhoods();
Assert.Equal(1, neighborhoods.Count());
Assert.Equal(12, neighborhoods.First().VcfVariantSites.Count());
}
public void Pisces_LowDepthTest()
{
List <ChrReference> chrRef = new List <ChrReference>()
{
new ChrReference()
{
Name = "chr19",
Sequence = "TTGTCAGTGCGCTTTTCCCAACACCACCTGCTCCGACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGGCGAAAAAAAAAAAAAAAAAAAAAAAAAA"
}
};
var options = new PiscesApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
//IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
MaxSizeMNV = 100,
OutputDirectory = TestPaths.LocalTestDataDirectory,
BamFilterParameters = new Domain.Options.BamFilterParameters()
{
MinimumBaseCallQuality = 20
},
VariantCallingParameters = new Domain.Options.VariantCallingParameters()
{
MinimumVariantQScore = 20,
MinimumCoverage = 1000,
},
VcfWritingParameters = new Domain.Options.VcfWritingParameters()
{
OutputGvcfFile = true,
}
};
var vcfFilePath = Path.ChangeExtension(options.BAMPaths[0], "genome.vcf");
var factory = new Factory(options);
IGenome genomeRef;
genomeRef = new MockGenome(chrRef, _genomeChr19);
var bp = new GenomeProcessor(factory, genomeRef);
bp.Execute(1);
List <VcfVariant> coverage1000results = VcfReader.GetAllVariantsInFile(vcfFilePath);
options = new PiscesApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
// IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
OutputDirectory = TestPaths.LocalTestDataDirectory,
VcfWritingParameters = new Domain.Options.VcfWritingParameters()
{
OutputGvcfFile = false,
}
};
factory = new Factory(options);
bp = new GenomeProcessor(factory, genomeRef);
bp.Execute(1);
List <VcfVariant> coverage10results = VcfReader.GetAllVariantsInFile(vcfFilePath);
// Assert.NotEqual(coverage1000results.Count, coverage10results.Count);
// Assert.Equal(coverage1000results.Count, 84);
// Assert.Equal(coverage10results.Count, 100);
}
private void Write_InFlow(bool threadByChr)
{
var bamFilePath = Path.Combine(UnitTestPaths.TestDataDirectory, "SBWriter_Sample_S1.bam");
var vcfFilePath = Path.Combine(UnitTestPaths.TestDataDirectory, "SBWriter_Sample_S1.genome.vcf");
var biasFilePath = Path.Combine(UnitTestPaths.TestDataDirectory, "SBWriter_Sample_S1.genome.ReadStrandBias.txt");
if (threadByChr)
{
biasFilePath = biasFilePath + "_chr19"; //Currently when threading by chrom we are outputting one bias file per chromsome. This is not a customer-facing deliverable and is a low-priority feature.
}
var expectedBiasResultsPath = Path.Combine(UnitTestPaths.TestDataDirectory, "Expected_Sample_S1.ReadStrandBias.txt");
var genomeDirectory = Path.Combine(UnitTestPaths.TestGenomesDirectory, "chr19");
var applicationOptions = new ApplicationOptions
{
BAMPaths = new[] { bamFilePath },
IntervalPaths = null,
GenomePaths = new[] { genomeDirectory },
OutputBiasFiles = true,
DebugMode = true,
OutputgVCFFiles = true,
};
// Using GenomeProcessor
//If OutputBiasFiles is true, should output one bias file per vcf
var factory = new MockFactoryWithDefaults(applicationOptions);
var genome = factory.GetReferenceGenome(genomeDirectory);
CreateAndExecuteProcessor(threadByChr, factory, genome);
Assert.True(File.Exists(biasFilePath));
//All variants that are present in VCF where ref!=alt should be included
var biasFileContents = File.ReadAllLines(biasFilePath);
var alleles = VcfReader.GetAllVariantsInFile(vcfFilePath);
var variantCalls = alleles.Where(a => a.VariantAlleles[0] != ".").ToList();
foreach (var variantCall in variantCalls)
{
Console.WriteLine(variantCall);
Assert.True(biasFileContents.Count(l => l.Split('\t')[0] == variantCall.ReferenceName &&
l.Split('\t')[1] == variantCall.ReferencePosition.ToString() &&
l.Split('\t')[2] == variantCall.ReferenceAllele &&
l.Split('\t')[3] == variantCall.VariantAlleles.First()) == 1);
}
foreach (var refCall in alleles.Where(a => a.VariantAlleles[0] == ".").ToList())
{
Assert.False(biasFileContents.Count(l => l.Split('\t')[0] == refCall.ReferenceName &&
l.Split('\t')[1] == refCall.ReferencePosition.ToString() &&
l.Split('\t')[2] == refCall.ReferenceAllele &&
l.Split('\t')[3] == refCall.VariantAlleles.First()) == 1);
}
//Bias files should have expected contents
var expectedBiasFileContents = File.ReadAllLines(expectedBiasResultsPath);
Assert.Equal(expectedBiasFileContents, biasFileContents);
//If OutputBiasFiles is false, should not output any bias files
File.Delete(biasFilePath);
applicationOptions.OutputBiasFiles = false;
factory = new MockFactoryWithDefaults(applicationOptions);
genome = factory.GetReferenceGenome(genomeDirectory);
CreateAndExecuteProcessor(threadByChr, factory, genome);
Assert.False(File.Exists(biasFilePath));
}
public void Execute(
string bamFilePath,
string vcfFilePath,
string intervalPath,
List <CalledAllele> expectedVariants,
List <ChrReference> fakeReferences = null,
bool doCheckVariants = true,
bool doCheckReferences = false,
int expectedNumCoveredPositions = 0,
bool threadByChr = false,
int doCountsOnly = 0,
bool doLog = false,
bool callMnvs = true,
ApplicationOptions applicationOptions = null,
bool collapse = true)
{
if (doCheckReferences)
{
vcfFilePath = Path.ChangeExtension(vcfFilePath, "genome.vcf");
}
if (applicationOptions == null)
{
applicationOptions = new ApplicationOptions
{
BAMPaths = new[] { bamFilePath },
IntervalPaths = string.IsNullOrEmpty(intervalPath) ? null : new[] { intervalPath },
GenomePaths = new[] { GenomeDirectory },
OutputgVCFFiles = doCheckReferences,
OutputBiasFiles = true,
DebugMode = doLog,
MinimumBaseCallQuality = 20,
CallMNVs = callMnvs,
MaxGapBetweenMNV = 10,
MaxSizeMNV = 15,
Collapse = collapse
};
}
Logger.TryOpenLog(applicationOptions.LogFolder, applicationOptions.LogFileName);
var factory = GetFactory(applicationOptions);
IGenome genome;
if (fakeReferences == null)
{
genome = factory.GetReferenceGenome(GenomeDirectory);
}
else
{
genome = new MockGenome(fakeReferences, GenomeDirectory);
}
if (threadByChr)
{
var processor = new GenomeProcessor(factory, genome, false);
processor.Execute(1);
}
else
{
var processor = new GenomeProcessor(factory, genome);
processor.Execute(1);
}
Logger.TryCloseLog();
var alleles = VcfReader.GetAllVariantsInFile(vcfFilePath);
var variantCalls = alleles.Where(a => a.VariantAlleles[0] != ".").ToList();
if (doCheckVariants)
{
if (doCountsOnly > 0)
{
Assert.Equal(variantCalls.Count(), doCountsOnly);
}
else
{
CheckVariants(variantCalls, expectedVariants);
}
}
if (doCheckReferences)
{
var referenceAlleles = alleles.Where(a => a.VariantAlleles[0] == ".").ToList();
// make sure no reference calls at variant positions
Assert.Equal(referenceAlleles.Count(),
alleles.Count(a => !variantCalls.Select(v => v.ReferencePosition).Contains(a.ReferencePosition)));
}
}
/// <summary>
/// MNV within overlap region's edge
/// </summary>
//[Fact]
//[Trait("Category", "ReadStitching")]
//public void MNV_PartialOverlap()
//{
// var outputFileName = "Mnv-PartialOverlap_S1.genome.vcf";
// var test = new AmpliconMnvTest()
// {
// StitchPairedReads = true,
// RequireXCTagToStitch = true,
// ReadLength = 30,
// ReferenceSequenceRelative = "GTTGGTCTTC" + "TATTTTATGCGAATTCTTCT" + "AAGATTCCCA",
// VariantPositionRelative = 9,
// ChangedSequence = "AAG",
// VariantDepth = 25,
// ReferenceDepth = 25
// };
// var expectedResults = new AmpliconTestResult()
// {
// VariantFrequency = 0.5f,
// TotalDepth = 50,
// VariantDepth = 25,
// ReferenceDepth = 25
// };
// ExecuteTest(test, outputFileName, expectedResults);
// test.RequireXCTagToStitch = false;
// ExecuteTest(test, outputFileName, expectedResults);
// // Note: don't test without stitch reads
// // this test would fail because the two reads would detect different variants
// // test.StitchPairedReads = false;
// // ExecuteTest(test, outputFileName, expectedResults);
// test.VariantDepth = 10;
// test.ReferenceDepth = 90;
// test.RequireXCTagToStitch = true;
// expectedResults = new AmpliconTestResult()
// {
// VariantFrequency = 0.1f,
// TotalDepth = 100,
// VariantDepth = 10,
// ReferenceDepth = 90
// };
// ExecuteTest(test, outputFileName, expectedResults);
// test.RequireXCTagToStitch = false;
// ExecuteTest(test, outputFileName, expectedResults);
//}
#region Helpers
private void ExecuteTest(AmpliconTest test, string outputFileName, AmpliconTestResult expectedResult)
{
var appOptions = new ApplicationOptions()
{
BAMPaths = new[] { string.Empty },
GenomePaths = new[] { _genomeChr19 },
OutputFolder = UnitTestPaths.TestDataDirectory,
OutputgVCFFiles = true,
StitchReads = test.StitchPairedReads,
RequireXCTagToStitch = test.RequireXCTagToStitch,
CallMNVs = true,
MaxSizeMNV = 3,
MaxGapBetweenMNV = 1
};
var vcfOutputPath = Path.Combine(appOptions.OutputFolder, outputFileName);
File.Delete(vcfOutputPath);
test.ChrOffset = CHR_OFFSET;
// test execution
var factory = new AmpliconTestFactory(test.ReferenceSequenceAbsolute, test.StitchPairedReads);
factory.ChrOffset = CHR_OFFSET;
if (test is AmpliconInsertionTest)
{
factory.StageInsertion(
test.ReadLength,
((AmpliconInsertionTest)test).InsertionSequence,
test.VariantPositionAbsolute,
test.VariantDepth,
test.ReferenceDepth);
}
else if (test is AmpliconDeletionTest)
{
factory.StageDeletion(
test.ReadLength,
((AmpliconDeletionTest)test).NumberDeletedBases,
test.VariantPositionAbsolute,
test.VariantDepth,
test.ReferenceDepth);
}
else if (test is AmpliconMnvTest)
{
factory.StageMnv(
test.ReadLength,
((AmpliconMnvTest)test).ChangedSequence,
test.VariantPositionAbsolute,
test.VariantDepth,
test.ReferenceDepth);
}
CallVariantsWithMockData(vcfOutputPath, appOptions, factory);
var results = GetResults(VcfReader.GetAllVariantsInFile(vcfOutputPath));
Assert.True(results.Count == 1);
var result = results[0];
if (test is AmpliconInsertionTest)
{
Assert.True(result.VariantAllele.Substring(1) == ((AmpliconInsertionTest)test).InsertionSequence);
}
else if (test is AmpliconDeletionTest)
{
Assert.True(result.ReferenceAllele.Length == ((AmpliconDeletionTest)test).NumberDeletedBases + 1);
}
else if (test is AmpliconMnvTest)
{
Assert.True(result.VariantAllele == ((AmpliconMnvTest)test).ChangedSequence);
}
Assert.True(result.Filters == "PASS");
Assert.True(result.Filters.Split(',').Count() == 1);
Assert.True(result.Position == test.VariantPositionAbsolute);
VerifyEqual(result.VariantFrequency, expectedResult.VariantFrequency, 0.1f);
VerifyEqual(result.TotalDepth, expectedResult.TotalDepth, 1f);
VerifyEqual(result.VariantDepth, expectedResult.VariantDepth, 1f);
VerifyEqual(result.ReferenceDepth, expectedResult.ReferenceDepth, 1f);
}
public void TestForStrandBiasOnStitchingScenarios(StitchingScenario scenario, string resultFile)
{
//limit the scope of concern for now.
if (scenario.ShouldRefStitch != true)
{
return;
}
//limit the scope of concern for now.
if (scenario.ShouldStitch != true)
{
return;
}
var resultsSummary = Path.Combine(Options.OutputFolder, StrandBiasSummaryFileName);
using (StreamWriter sw = new StreamWriter(resultsSummary, true))
{
var sb = new StringBuilder(
string.Join(",", DateTime.Today.ToShortDateString(),
DateTime.Now.ToLongTimeString(),
scenario.Category, scenario.Id));
try
{
if (!Directory.Exists(Options.OutputFolder))
{
Directory.CreateDirectory(Options.OutputFolder);
}
var factory = new AmpliconTestFactory(new string('A', 100), sourceIsStitched: true);
byte qualityForAll = 30;
int numVariantCounts = 2; // 10;
int numReferenceCounts = 2; // 90;
var varRead = BuildRead(scenario.OutputRead1, qualityForAll, StageMNVdata(scenario));
var refRead = BuildRead(scenario.OutputRefRead1, qualityForAll, NoMNVdata(scenario));
if (refRead == null)
{
return;
}
factory.StageStitchedVariant(
varRead, numVariantCounts,
refRead, numReferenceCounts);
var outputFileName = string.Format("{0}_{1}.vcf", scenario.Category, scenario.Id);
var vcfOutputPath = Path.Combine(Options.OutputFolder, outputFileName);
var biasOutputPath = StrandBiasFileWriter.GetBiasFilePath(vcfOutputPath);
File.Delete(vcfOutputPath);
File.Delete(biasOutputPath);
StitchedReadBiasHelper.CallStrandedVariantsWithMockData(vcfOutputPath, Options, factory);
var varResults = StitchedReadBiasHelper.GetResults(VcfReader.GetAllVariantsInFile(vcfOutputPath));
var biasResults = StitchedReadBiasHelper.GetStrandResultsFromFile(biasOutputPath);
var observedFrequency = (varResults.Count == 0) ? "0": "";
var observedSB = (biasResults.Count == 0) ? "FN": "";
for (int i = 0; i < varResults.Count; i++)
{
var varResult = varResults[i];
if (i != 0)
{
observedFrequency += ";";
}
observedFrequency += varResult.VariantFrequency;
}
for (int i = 0; i < biasResults.Count; i++)
{
var biasResult = biasResults[i];
if (i != 0)
{
observedSB += ";";
}
observedSB += biasResult.HasStrandBias;
//there should be no SB on our current set of stitched scenarios.
Assert.True(!biasResult.HasStrandBias);
}
var expectedValues = new List <string>()
{
"1", scenario.Frequency, scenario.ShouldBias
};
var observedValues = new List <string>()
{
varResults.Count.ToString(), observedFrequency, observedSB
};
sb.Append(GetResultString(expectedValues, observedValues));
sw.WriteLine(sb.ToString());
}
catch (Exception ex)
{
sb.Append(",Fail: " + ex);
sw.WriteLine(sb.ToString());
}
}
}
public void UnpackAlleles()
{
//two example vcf files that have been "crushed".
var crushedVcf1 = Path.Combine(TestPaths.LocalTestDataDirectory, "VcfFileWriterTests_Crushed_Padded_expected.vcf");
var crushedVcf2 = Path.Combine(TestPaths.LocalTestDataDirectory, "crushed.genome.vcf");
var vcfVariants1 = VcfReader.GetAllVariantsInFile(crushedVcf1);
var vcfVariants2 = VcfReader.GetAllVariantsInFile(crushedVcf2);
Assert.Equal(7, vcfVariants1.Count);
Assert.Equal(90, vcfVariants2.Count);
// 1/2 variants
var hetAlt1 = vcfVariants1[5];
var hetAlt2 = vcfVariants2[3];
var hetAlt1next = vcfVariants1[6];
var hetAlt2next = vcfVariants2[4];
Assert.Equal(1, hetAlt1.Genotypes.Count);
Assert.Equal(1, hetAlt2.Genotypes.Count);
Assert.Equal(2, hetAlt1.VariantAlleles.Count());
Assert.Equal(2, hetAlt2.VariantAlleles.Count());
Assert.Equal("2387,2000", hetAlt1.Genotypes[0]["AD"]);
Assert.Equal("0.8133", hetAlt1.Genotypes[0]["VF"]);
Assert.Equal("254,254", hetAlt2.Genotypes[0]["AD"]);
Assert.Equal("AA", hetAlt1.ReferenceAllele);
Assert.Equal("GA", hetAlt1.VariantAlleles[0]);
Assert.Equal("G", hetAlt1.VariantAlleles[1]);
Assert.Equal(".", hetAlt1next.VariantAlleles[0]);
Assert.Equal("0", hetAlt1next.Genotypes[0]["AD"]);
Assert.Equal("532", hetAlt2next.Genotypes[0]["AD"]);
Assert.Equal(10, hetAlt1.ReferencePosition);
Assert.Equal(223906731, hetAlt2.ReferencePosition);
Assert.Equal(10 + 1, hetAlt1next.ReferencePosition);
Assert.Equal(223906731 + 1, hetAlt2next.ReferencePosition);
var unpackedVariants1 = VcfVariantUtilities.UnpackVariants(vcfVariants1);
var unpackedVariants2 = VcfVariantUtilities.UnpackVariants(vcfVariants2);
Assert.Equal(8, unpackedVariants1.Count);
Assert.Equal(91, unpackedVariants2.Count);
hetAlt1 = unpackedVariants1[5];
hetAlt2 = unpackedVariants2[3];
hetAlt1next = unpackedVariants1[6];
hetAlt2next = unpackedVariants2[4];
//example one:
//total depth = 5394, total variant count = 2387 + 2000 = 4387
//so, ref counts ~1007.
//example two:
//total depth = 532, total variant count = 254 + 254 = 508
//so, ref counts ~24.
Assert.Equal(1, hetAlt1.Genotypes.Count);
Assert.Equal(1, hetAlt2.Genotypes.Count);
Assert.Equal("1007,2387", hetAlt1.Genotypes[0]["AD"]);
Assert.Equal("24,254", hetAlt2.Genotypes[0]["AD"]);
Assert.Equal("0.4425", hetAlt1.Genotypes[0]["VF"]);
Assert.Equal(1, hetAlt1.VariantAlleles.Count());
Assert.Equal(1, hetAlt2.VariantAlleles.Count());
Assert.Equal(1, hetAlt1next.VariantAlleles.Count());
Assert.Equal(1, hetAlt2next.VariantAlleles.Count());
Assert.Equal("1007,2000", hetAlt1next.Genotypes[0]["AD"]);
Assert.Equal("24,254", hetAlt2next.Genotypes[0]["AD"]);
Assert.Equal("AA", hetAlt1.ReferenceAllele);
Assert.Equal("GA", hetAlt1.VariantAlleles[0]);
Assert.Equal("G", hetAlt1next.VariantAlleles[0]);
Assert.Equal("0.3708", hetAlt1next.Genotypes[0]["VF"]);
Assert.Equal(10, hetAlt1.ReferencePosition);
Assert.Equal(223906731, hetAlt2.ReferencePosition);
Assert.Equal(10, hetAlt1next.ReferencePosition);
Assert.Equal(223906731, hetAlt2next.ReferencePosition);
}
public void VennVcf_CombineTwoPoolVariants_ProbePoolBias_Tests()
{
//this is from an issue anita had where a variant was in one pool at 1%, the other at 0%, and showed up as 6% in the combined pool.
var outDir = TestPaths.LocalScratchDirectory;
var VcfPathRoot = _TestDataPath;
string VcfPath_PoolA = Path.Combine(VcfPathRoot, "small_S14.genome.vcf");
string VcfPath_PoolB = Path.Combine(VcfPathRoot, "small_S17.genome.vcf");
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = Path.Combine(outDir, "Consensus.vcf");
parameters.OutputDirectory = outDir;
if (File.Exists(parameters.ConsensusFileName))
{
File.Delete(parameters.ConsensusFileName);
}
VennProcessor Venn = new VennProcessor(new string[] { VcfPath_PoolA, VcfPath_PoolB }, parameters);
Venn.DoPairwiseVenn(false);
Assert.Equal(File.Exists(parameters.ConsensusFileName), true);
List <VcfVariant> CombinedVariants = VcfReader.GetAllVariantsInFile(parameters.ConsensusFileName);
List <VcfVariant> AandBVariants = VcfReader.GetAllVariantsInFile(Path.Combine(outDir, "small_S14_and_S17.vcf"));
List <VcfVariant> BandAVariants = VcfReader.GetAllVariantsInFile(Path.Combine(outDir, "small_S17_and_S14.vcf"));
List <VcfVariant> AnotBVariants = VcfReader.GetAllVariantsInFile(Path.Combine(outDir, "small_S14_not_S17.vcf"));
List <VcfVariant> BnotAVariants = VcfReader.GetAllVariantsInFile(Path.Combine(outDir, "small_S17_not_S14.vcf"));
//poolA
//chr1 115258743 . A . 100 PASS DP=35354 GT:GQ:AD:VF:NL:SB 0/0:100:30256:0.1442:20:-100.0000
//chr1 115258743 . AC TT 100 PASS DP=35354 GT:GQ:AD:VF:NL:SB 0/1:100:30720,4634:0.1311:20:-100.0000
//chr1 115258744 . C . 100 PASS DP=35253 GT:GQ:AD:VF:NL:SB 0/0:100:30277:0.1412:20:-100.0000
//chr1 115258745 . C . 100 PASS DP=35160 GT:GQ:AD:VF:NL:SB 0/0:100:35130:0.0009:20:-100.0000
//poolB
//chr1 115258743 . AC TT 100 PASS DP=49612 GT:GQ:AD:VF:NL:SB 0/1:100:44202,5410:0.1090:20:-100.0000
//chr1 115258743 . A T 100 PASS DP=49612 GT:GQ:AD:VF:NL:SB 0/1:100:43362,670:0.0135:20:-46.0807
//chr1 115258744 . C T 24 PASS DP=49902 GT:GQ:AD:VF:NL:SB 0/1:24:43905,560:0.0112:20:-8.3857
//when we had bug:
//chr1 115258743 . AC TT 100.00 PASS DP=84966 GT:GQ:AD:VF:NL: 0/1:100:74922,10044:0.1182:20:-100:-100.0000:100
//chr1 115258743 . A T 100.00 PB;LowVF DP=49612 GT:GQ:AD:VF:NL: ./.:100:43362,670:0.0135:20:-46.0807:0.0000:100
//chr1 115258743 . A . 100.00 PASS DP=35354 GT:GQ:AD:VF:NL: 0/0:100:30256:0.1442:20:-100.0000:-100.0000:100
//chr1 115258744 . C T 100.00 PB DP=85155 GT:GQ:AD:VF:NL: 0/1:100:74182,5536:0.0650:20:-
//(issue#1) at 743 we had a A->. in only one pool. It should be marked as BIAS and not PASS.
//(issue#2) at 744 we had a C->T at 6% when it should be at ~0%, and called as a ref.
string VFstring = "";
VcfVariant FunnyResult0 = CombinedVariants[3];
VFstring = FunnyResult0.Genotypes[0]["VF"];
Assert.Equal(VFstring, "0.144");
Assert.Equal(FunnyResult0.Filters, "PB");
Assert.Equal(FunnyResult0.ReferenceAllele, "A");
Assert.Equal(FunnyResult0.VariantAlleles[0], ".");
//this used to be a reference as a pass, even though it was only called in one pool.
VcfVariant FunnyResult = CombinedVariants[6];
Assert.Equal(FunnyResult.ReferencePosition, 115258744);
VFstring = FunnyResult.Genotypes[0]["VF"];
Assert.Equal(VFstring, "0.129");
Assert.Equal(FunnyResult.Filters, "PASS");
Assert.Equal(FunnyResult.ReferenceAllele, "C");
Assert.Equal(FunnyResult.VariantAlleles[0], ".");
//when we had the bug, this used to get called at 6%.
//now, check the Venn functionality:
Assert.Equal(2, AandBVariants.Count());
Assert.Equal(2, BandAVariants.Count());
Assert.Equal(2, AnotBVariants.Count());
Assert.Equal(0, BnotAVariants.Count());
Assert.Equal(115258743, AandBVariants[0].ReferencePosition);
Assert.Equal("AC", AandBVariants[0].ReferenceAllele);
Assert.Equal("TT", AandBVariants[0].VariantAlleles[0]);
Assert.Equal(115258747, AandBVariants[1].ReferencePosition);
Assert.Equal("C", AandBVariants[1].ReferenceAllele);
Assert.Equal("T", AandBVariants[1].VariantAlleles[0]);
Assert.Equal(115258743, BandAVariants[0].ReferencePosition);
Assert.Equal("AC", BandAVariants[0].ReferenceAllele);
Assert.Equal("TT", BandAVariants[0].VariantAlleles[0]);
Assert.Equal(115258747, BandAVariants[1].ReferencePosition);
Assert.Equal("C", BandAVariants[1].ReferenceAllele);
Assert.Equal("T", BandAVariants[1].VariantAlleles[0]);
Assert.Equal(115258743, AnotBVariants[0].ReferencePosition);
Assert.Equal("A", AnotBVariants[0].ReferenceAllele);
Assert.Equal("T", AnotBVariants[0].VariantAlleles[0]);
Assert.Equal(115258744, AnotBVariants[1].ReferencePosition);
Assert.Equal("C", AnotBVariants[1].ReferenceAllele);
Assert.Equal("T", AnotBVariants[1].VariantAlleles[0]);
}
public void VennVcf_CombineTwoPoolVariants_RulesAthroughD_Tests()
{
var outDir = TestPaths.LocalScratchDirectory;
var VcfPathRoot = _TestDataPath;
string OutputPath = Path.Combine(outDir, "outEandF.vcf");
if (File.Exists(OutputPath))
{
File.Delete(OutputPath);
}
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = OutputPath;
string VcfPath_PoolA = Path.Combine(VcfPathRoot, "09H-03403-MT1-1_S7.genome.vcf");
List <CalledAllele> PoolAVariants = VcfVariantUtilities.Convert(VcfReader.GetAllVariantsInFile(VcfPath_PoolA)).ToList();
string VcfPath_PoolB = Path.Combine(VcfPathRoot, "09H-03403-MT1-1_S8.genome.vcf");
List <CalledAllele> PoolBVariants = VcfVariantUtilities.Convert(VcfReader.GetAllVariantsInFile(VcfPath_PoolB)).ToList();
CalledAllele VariantA = PoolAVariants[0];
CalledAllele VariantB = PoolBVariants[0];
List <CalledAllele[]> pairs = VennProcessor.SelectPairs(
new List <CalledAllele>()
{
VariantA
},
new List <CalledAllele>
{
VariantB
});
VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(pairs[0][0], pairs[0][1]);
ConsensusBuilder consensusBuilder = new ConsensusBuilder("", parameters);
CalledAllele Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
//Rule "A" test
//A if combined VF<1% and less than 2.6% in each pool, call REF
//(note, we were Alt in one pool and ref in another)
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(VariantA.Frequency, 0.9979, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantB.Frequency, 0.0173, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(Consensus.Frequency, 0.9907, 4);
Assert.Equal(Consensus.VariantQscore, 100);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
}); //<-low VF tag will NOT added by post-processing b/c is ref call
//B if combined VF<1% and more than 2.6% in one pool, call NO CALL
VariantA = PoolAVariants[1];
VariantB = PoolBVariants[1];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.0776, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(VariantB.Frequency, 0.9989, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall);
Assert.Equal(Consensus.Frequency, 0.0070, 4);
Assert.Equal(Consensus.VariantQscore, 0);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType>
{
Pisces.Domain.Types.FilterType.PoolBias
}); //<-low VF tag will also get added by post-processing
//Rule "Ca" test
//C-a if combined 1%<VF<2.6%
// and more than 2.6% in one pool and less than 1% in the other, call NO CALL w/PB
VariantA = PoolAVariants[2];
VariantB = PoolBVariants[2];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.0367, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(VariantB.Frequency, 0.9976, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall);
Assert.Equal(Consensus.Frequency, 0.0117, 4);
Assert.Equal(Consensus.VariantQscore, 23);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
Pisces.Domain.Types.FilterType.PoolBias
});
//Rule "Cb" test
//C-a if combined 1%<VF<2.6%
// and more than 2.6% in one pool and between 1% and 2.6% in the other, call NO CALL w/ no PB
VariantA = PoolAVariants[3];
VariantB = PoolBVariants[3];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.01725, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantB.Frequency, 0.03667, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.AgreedOnAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall);
Assert.Equal(Consensus.Frequency, 0.02347, 4);
Assert.Equal(Consensus.VariantQscore, 100);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
}); //<-low VF tag will also get added by post-processing
//Rule "D" test
//D if combined VF>=2.6% call VARIANT (PB if only present in one pool, using 1% as the cutoff)
VariantA = PoolAVariants[4];
VariantB = PoolBVariants[4];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.2509, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantB.Frequency, 0.0367, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.AgreedOnAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(Consensus.Frequency, 0.1716, 4);
Assert.Equal(Consensus.VariantQscore, 100);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
}); //<-low VF tag will also get set by post processor
}
public void StitchedCollapsedBamGroundTruth()
{
// SNP ground truth from TingTing
var bamFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "collapsed.test.stitched.bam");
var functionalTestRunner = new SomaticVariantCallerFunctionalTestSetup();
functionalTestRunner.GenomeDirectory = Path.Combine(TestPaths.SharedGenomesDirectory, "chr1");
var appOptions = new PiscesApplicationOptions
{
BAMPaths = new[] { bamFilePath },
IntervalPaths = null,
GenomePaths = new[] { Path.Combine(TestPaths.SharedGenomesDirectory, "chr1") },
OutputBiasFiles = true,
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
MaxSizeMNV = 100,
MaxGapBetweenMNV = 10,
NoiseModelHalfWindow = 1,
BamFilterParameters = new Domain.Options.BamFilterParameters()
{
MinimumBaseCallQuality = 20,
MinimumMapQuality = 1,
OnlyUseProperPairs = false,
},
VariantCallingParameters = new Domain.Options.VariantCallingParameters()
{
MaximumVariantQScore = 100,
MinimumVariantQScoreFilter = 30,
MinimumVariantQScore = 20,
MinimumCoverage = 10,
MinimumFrequency = 0.01f,
FilterOutVariantsPresentOnlyOneStrand = false,
ForcedNoiseLevel = -1,
NoiseModel = NoiseModel.Flat,
StrandBiasModel = StrandBiasModel.Extended,
},
VcfWritingParameters = new Domain.Options.VcfWritingParameters()
{
OutputGvcfFile = true,
ReportRcCounts = true,
ReportTsCounts = true
}
};
// Time to build the fake sequences for testing.
var mockChrRef = new List <ChrReference>()
{
new ChrReference()
{
// position 9770498 ~ 9770669
Name = "chr1",
Sequence = new string('N', 9770498 - 1) + "GAAGTAACAACGCAGGATGCCCCCTGGGGTGGACTGCCCCATGGAATTCTGGACCAAGGAGGAGAATCAGAGCGTTGTGGTTGACTTCCTGCTGCCCACAGGGGTCTACCTGAACTTCCCTGTGTCCCGCAATGCCAACCTCAGCACCATCAAGCAGGTATGGCCTCCATC"
}
};
var expectedAlleles = new List <CalledAllele>
{
new CalledAllele(AlleleCategory.Snv)
{
ReferencePosition = 9770596,
ReferenceAllele = "C",
AlternateAllele = "A",
Chromosome = "chr1"
}
};
functionalTestRunner.Execute(bamFilePath, Path.ChangeExtension(bamFilePath, "genome.vcf"), null, expectedAlleles, mockChrRef, applicationOptions: appOptions);
var truthvcfFilePath = Path.Combine(Path.GetDirectoryName(appOptions.BAMPaths[0]), "test_truth.stitched.genome.vcf");
var stitchedCollapsedTruth = VcfReader.GetAllVariantsInFile(truthvcfFilePath);
var stitchedCollapsedResults = VcfReader.GetAllVariantsInFile(Path.ChangeExtension(bamFilePath, "genome.vcf"));
foreach (var variantTruth in stitchedCollapsedTruth)
{
var variantActual = stitchedCollapsedResults.First(x => x.ReferencePosition == variantTruth.ReferencePosition);
Assert.NotNull(variantActual);
Assert.Equal(variantTruth.Genotypes[0]["US"], variantActual.Genotypes[0]["US"]);
}
}
public void VennVcf_CombineTwoPoolVariants_RulesEandF_Tests()
{
//Rule "E" test (ie an Alt+ref call converges to a REf, and we also had a ref call following it)
//E if we end up with multiple REF calls for the same loci, combine those .VCF lines into one ref call.
//Rule "F" test (ie various alt calls all ended up as no-call. we dont want multiple no call lines in the vcf.)
//F if we end up with multiple NOCALL calls for the same loci, leave those .VCF lines separate
var outDir = TestPaths.LocalScratchDirectory;
var VcfPathRoot = _TestDataPath;
string VcfPath_PoolA = Path.Combine(VcfPathRoot, "RulesEandF_S1.genome.vcf");
string VcfPath_PoolB = Path.Combine(VcfPathRoot, "RulesEandF_S2.genome.vcf");
string OutputPath = Path.Combine(outDir, "outEandF.vcf");
if (File.Exists(OutputPath))
{
File.Delete(OutputPath);
}
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = OutputPath;
parameters.OutputDirectory = outDir;
VennProcessor VennVcf = new VennProcessor(
new string[] { VcfPath_PoolA, VcfPath_PoolB }, parameters);
VennVcf.DoPairwiseVenn(false);
Assert.Equal(File.Exists(OutputPath), true);
List <VcfVariant> PoolAVariants = VcfReader.GetAllVariantsInFile(VcfPath_PoolA);
List <VcfVariant> PoolBVariants = VcfReader.GetAllVariantsInFile(VcfPath_PoolB);
List <VcfVariant> CombinedVariants = VcfReader.GetAllVariantsInFile(OutputPath);
//Rule "E" test (ie an Alt+ref call converges to a REf, and we also had a ref call following it)
//E if we end up with multiple REF calls for the same loci, combine those .VCF lines into one ref call.
VcfVariant VariantA_1 = PoolAVariants[0];
Assert.Equal(VariantA_1.Genotypes[0]["GT"], "0/0");
Assert.Equal(VariantA_1.Genotypes[0]["VF"], "0.0021");
Assert.Equal(VariantA_1.Quality, 100);
Assert.Equal(VariantA_1.Filters, "PASS");
Assert.Equal(VariantA_1.ReferencePosition, 25378561);
VcfVariant VariantA_2 = PoolAVariants[1];
Assert.Equal(VariantA_2.ReferencePosition, 25378562);
VcfVariant VariantB_1 = PoolBVariants[0];
Assert.Equal(VariantB_1.Genotypes[0]["GT"], "0/1");
Assert.Equal(VariantB_1.Genotypes[0]["VF"], "0.0173");
Assert.Equal(VariantB_1.Quality, 100);
Assert.Equal(VariantB_1.Filters, "PASS");
Assert.Equal(VariantB_1.ReferencePosition, 25378561);
VcfVariant VariantB_2 = PoolBVariants[1];
Assert.Equal(VariantB_2.Genotypes[0]["GT"], "0/0");
Assert.Equal(VariantB_2.Genotypes[0]["VF"], "0.0021");
Assert.Equal(VariantB_2.Quality, 100);
Assert.Equal(VariantB_2.Filters, "PASS");
Assert.Equal(VariantB_2.ReferencePosition, 25378561);
VcfVariant Consensus_1 = CombinedVariants[0];
Assert.Equal(Consensus_1.Genotypes[0]["GT"], "0/0");
Assert.Equal(Consensus_1.Genotypes[0]["VF"], "0.009"); //slightly improved from .008
Assert.Equal(Consensus_1.Quality, 100);
Assert.Equal(Consensus_1.Filters, "PASS"); //<-low VF tag will NOT added by post-processing b/c is ref call
Assert.Equal(Consensus_1.ReferencePosition, 25378561);
VcfVariant Consensus_2 = CombinedVariants[1];
Assert.Equal(Consensus_2.ReferencePosition, 25378562);
//Rule "F" test (ie various alt calls all ended up as no-call.
//F if we end up with multiple NOCALL calls for the same loci, leave those .VCF lines separate
VariantA_1 = PoolAVariants[1];
Assert.Equal(VariantA_1.Genotypes[0]["GT"], "0/1");
Assert.Equal(VariantA_1.Genotypes[0]["VF"], "0.0725");
Assert.Equal(VariantA_1.Quality, 100);
Assert.Equal(VariantA_1.Filters, "PASS");
Assert.Equal(VariantA_1.ReferencePosition, 25378562);
VariantA_2 = PoolAVariants[2];
Assert.Equal(VariantA_2.Genotypes[0]["GT"], "0/1");
Assert.Equal(VariantA_2.Genotypes[0]["VF"], "0.0725");
Assert.Equal(VariantA_2.Quality, 100);
Assert.Equal(VariantA_2.Filters, "PASS");
Assert.Equal(VariantA_2.ReferencePosition, 25378562);
VcfVariant VariantA_3 = PoolAVariants[3];
Assert.Equal(VariantA_3.Genotypes[0]["GT"], "0/1");
Assert.Equal(VariantA_3.Genotypes[0]["VF"], "0.0725");
Assert.Equal(VariantA_3.Quality, 100);
Assert.Equal(VariantA_3.Filters, "PASS");
Assert.Equal(VariantA_3.ReferencePosition, 25378562);
VariantB_1 = PoolBVariants[2];
Assert.Equal(VariantB_1.Genotypes[0]["GT"], "0/0");
Assert.Equal(VariantB_1.Genotypes[0]["VF"], "0.0024");
Assert.Equal(VariantB_1.Quality, 100);
Assert.Equal(VariantB_1.Filters, "PASS");
Assert.Equal(VariantB_1.ReferencePosition, 25378562);
VariantB_2 = PoolBVariants[3];
Assert.Equal(VariantB_2.ReferencePosition, 25378563);
Consensus_1 = CombinedVariants[1];
Assert.Equal(Consensus_1.ReferencePosition, 25378562);
Assert.Equal(Consensus_1.Genotypes[0]["GT"], "./.");
Assert.Equal(Consensus_1.Genotypes[0]["VF"], "0.007");
Assert.Equal(Consensus_1.Quality, 0);
Assert.Equal(Consensus_1.Filters, "PB"); //<-low VF tag will also get added by post-processing
Assert.Equal(Consensus_1.ReferenceAllele, "C");
Assert.Equal(Consensus_1.VariantAlleles[0], "T");
Consensus_2 = CombinedVariants[2];
Assert.Equal(Consensus_2.ReferencePosition, 25378562);
Assert.Equal(Consensus_2.Genotypes[0]["GT"], "./.");
Assert.Equal(Consensus_2.Genotypes[0]["VF"], "0.007");
Assert.Equal(Consensus_2.Quality, 0);
Assert.Equal(Consensus_2.Filters, "PB"); //<-low VF tag will also get added by post-processing
Assert.Equal(Consensus_2.ReferenceAllele, "C");
Assert.Equal(Consensus_2.VariantAlleles[0], "TT");
VcfVariant Consensus_3 = CombinedVariants[3];
Assert.Equal(Consensus_3.ReferencePosition, 25378562);
Assert.Equal(Consensus_3.Genotypes[0]["GT"], "./.");
Assert.Equal(Consensus_3.Genotypes[0]["VF"], "0.007");
Assert.Equal(Consensus_3.Quality, 0);
Assert.Equal(Consensus_3.Filters, "PB"); //<-low VF tag will also get added by post-processing
Assert.Equal(Consensus_3.ReferenceAllele, "CC");
Assert.Equal(Consensus_3.VariantAlleles[0], "T");
VcfVariant Consensus_4 = CombinedVariants[4];
Assert.Equal(Consensus_4.ReferencePosition, 25378563);
if (File.Exists(OutputPath))
{
File.Delete(OutputPath);
}
}
