public static List <AmpliconTestResult> GetResults(List <VcfVariant> vcfResults)
{
var results = new List <AmpliconTestResult>();
var allVariants = vcfResults.Where(x => x.VariantAlleles[0] != ".");
foreach (var variant in allVariants)
{
var result = new AmpliconTestResult()
{
Position = variant.ReferencePosition,
ReferenceAllele = variant.ReferenceAllele,
VariantAllele = variant.VariantAlleles[0]
};
var genotype = variant.Genotypes[0];
result.VariantFrequency = float.Parse(genotype["VF"]);
var ADTokens = genotype["AD"].Split(',');
result.ReferenceDepth = float.Parse(ADTokens[0]);
result.VariantDepth = float.Parse(ADTokens[1]);
result.TotalDepth = float.Parse(variant.InfoFields["DP"]);
result.Filters = variant.Filters;
results.Add(result);
}
return(results);
}
public static List <AmpliconTestResult> GetResults(List <CalledAllele> vcfResults)
{
var results = new List <AmpliconTestResult>();
var allVariants = vcfResults.Where(x => x.AlternateAllele != ".");
foreach (var variant in allVariants)
{
var result = new AmpliconTestResult()
{
Position = variant.ReferencePosition,
ReferenceAllele = variant.ReferenceAllele,
VariantAllele = variant.AlternateAllele
};
var genotype = variant.Genotype;
result.VariantFrequency = variant.Frequency;
result.ReferenceDepth = variant.ReferenceSupport;
result.VariantDepth = variant.AlleleSupport;
result.TotalDepth = variant.TotalCoverage;
result.Filters = variant.Filters;
results.Add(result);
}
return(results);
}
public void MNV_Edge()
{
var outputFileName = "Mnv-Edge_S1.genome.vcf";
var test = new AmpliconMnvTest()
{
StitchPairedReads = true,
RequireXCTagToStitch = true,
ReadLength = 30,
ReferenceSequenceRelative = "GTTGGTCTAT" + "TATTTTATGCGAATTCTTCT" + "AAGATTCCCA",
VariantPositionRelative = 9,
ChangedSequence = "CC",
VariantDepth = 25,
ReferenceDepth = 75
};
var expectedResults = new AmpliconTestResult()
{
VariantFrequency = 0.25f,
TotalDepth = 100,
VariantDepth = 25f,
ReferenceDepth = 75f
};
ExecuteTest(test, outputFileName, expectedResults);
test.RequireXCTagToStitch = false;
ExecuteTest(test, outputFileName, expectedResults);
test.StitchPairedReads = false;
ExecuteTest(test, outputFileName, expectedResults);
// change vaf
test.VariantDepth = 10;
test.ReferenceDepth = 40;
test.RequireXCTagToStitch = true;
test.StitchPairedReads = true;
expectedResults = new AmpliconTestResult()
{
VariantFrequency = 0.2f,
TotalDepth = 50,
VariantDepth = 10f,
ReferenceDepth = 40f
};
ExecuteTest(test, outputFileName, expectedResults);
// other side
test.VariantPositionRelative = 31;
ExecuteTest(test, outputFileName, expectedResults);
}
public void Deletion_Edge()
{
var outputFileName = "Deletion-Edge_S1.genome.vcf";
var test = new AmpliconDeletionTest()
{
StitchPairedReads = true,
RequireXCTagToStitch = true,
ReadLength = 30,
ReferenceSequenceRelative = "GTTGGTCTTC" + "TATTTTATGCGAATTCTTCT" + "AAGATTCCCA",
VariantPositionRelative = 5,
NumberDeletedBases = 5,
VariantDepth = 75,
ReferenceDepth = 25
};
var expectedResults = new AmpliconTestResult()
{
VariantFrequency = 0.75f,
TotalDepth = 100f,
VariantDepth = 75f,
ReferenceDepth = 25f
};
ExecuteTest(test, outputFileName, expectedResults);
test.RequireXCTagToStitch = false;
ExecuteTest(test, outputFileName, expectedResults);
test.StitchPairedReads = false;
ExecuteTest(test, outputFileName, expectedResults);
// change vaf and other side
test.VariantDepth = 10;
test.ReferenceDepth = 40;
test.VariantPositionRelative = 30;
test.RequireXCTagToStitch = true;
expectedResults = new AmpliconTestResult()
{
VariantFrequency = 0.2f,
TotalDepth = 50,
VariantDepth = 10f,
ReferenceDepth = 40f
};
ExecuteTest(test, outputFileName, expectedResults);
}
public void Insertion_WTFullOverlap_VarFullOverlap()
{
var outputFileName = "Insertion-WTFullOverlap-VarFullOverlap_S1.genome.vcf";
var test = new AmpliconInsertionTest()
{
StitchPairedReads = true,
RequireXCTagToStitch = true,
ReadLength = 30,
ReferenceSequenceRelative = "GTTGGTCTTC" + "TATTTTATGCGAATTCTTCT" + "AAGATTCCCA",
InsertionSequence = "ATACC",
VariantPositionRelative = 23,
VariantDepth = 25,
ReferenceDepth = 25
};
var expectedResults = new AmpliconTestResult()
{
VariantFrequency = 0.5f,
TotalDepth = 50f,
VariantDepth = 25f,
ReferenceDepth = 25f,
};
ExecuteTest(test, outputFileName, expectedResults);
test.RequireXCTagToStitch = false;
ExecuteTest(test, outputFileName, expectedResults);
test.VariantDepth = 60;
test.ReferenceDepth = 150;
test.RequireXCTagToStitch = true;
test.StitchPairedReads = true;
expectedResults = new AmpliconTestResult()
{
VariantFrequency = 0.29f,
TotalDepth = 210,
VariantDepth = 60,
ReferenceDepth = 150,
};
ExecuteTest(test, outputFileName, expectedResults);
}
/// <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);
}