public void RecalibrateVcf()
{
var vcfPath = Path.Combine(UnitTestPaths.TestDataDirectory, "Test.vcf");
var countsPath = Path.Combine(UnitTestPaths.TestDataDirectory, "Expected.counts");
var outFile = Path.Combine(UnitTestPaths.TestDataDirectory, "Test.vcf.recal");
var expectedFile = Path.Combine(UnitTestPaths.TestDataDirectory, "ExpectedTest.vcf.recal");
if (File.Exists(outFile))
{
File.Delete(outFile);
}
QualityRecalibration.Recalibrate(vcfPath, countsPath, 30, 0, 66, -1);
Assert.True(File.Exists(outFile));
var observedLines = File.ReadAllLines(outFile);
var expectedLines = File.ReadAllLines(expectedFile);
Assert.Equal(expectedLines.Length, observedLines.Length);
for (int i = 0; i < expectedLines.Length; i++)
{
Assert.Equal(expectedLines[0], observedLines[0]);
}
}
public void RecalibrateCleanVcf()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Test.vcf");
var countsPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Clean.counts");
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "RecalibrateDirtyVcf");
var outFile = Path.Combine(outDir, "Test.vcf.recal");
var expectedFile = Path.Combine(TestPaths.LocalTestDataDirectory, "ExpectedTest.vcf.recal");
if (File.Exists(outFile))
{
File.Delete(outFile);
}
Logger.OpenLog(TestPaths.LocalScratchDirectory, "RecalibrateCleanVcfLog.txt", true);
QualityRecalibration.Recalibrate(vcfPath, countsPath, outDir, 30, 0, 66, -1, null);
Logger.CloseLog();
//no recalibration should occur for a clean file.
Assert.True(!File.Exists(outFile));
//redirect log incase any other thread is logging here.
var SafeLogDir = TestPaths.LocalScratchDirectory;
Logger.OpenLog(SafeLogDir, "DefaultLog.txt", true);
Logger.CloseLog();
}
public void RecalibrateDirtyVcf()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "TestWithArtifacts.vcf");
var countsPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Dirty.counts");
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "RecalibrateDirtyVcf");
var outFile = Path.Combine(outDir, "TestWithArtifacts.vcf.recal");
var expectedFile = Path.Combine(TestPaths.LocalTestDataDirectory, "ExpectedDirty.vcf.recal");
if (File.Exists(outFile))
{
File.Delete(outFile);
}
Logger.OpenLog(outDir, "RecalibrateDirtyVcfLog.txt", true);
QualityRecalibration.Recalibrate(vcfPath, countsPath, outDir, 30, 0, 66, -1, "\"-vcf TestWithArtifacts.vcf\"");
Logger.CloseLog();
Assert.True(File.Exists(outFile));
TestUtilities.TestHelper.CompareFiles(outFile, expectedFile);
//redirect log incase any other thread is logging here.
var SafeLogDir = TestPaths.LocalScratchDirectory;
Logger.OpenLog(SafeLogDir, "DefaultLog.txt", true);
Logger.CloseLog();
//delete our log
File.Delete(outFile);
}
public void CanSkipVcfLineTests()
{
//lines we can skip
string skip1 = "chr4\t169663557\t.\tT\t.\t100\tPASS\tDP=23\tGT:GQ:AD:DP:VF:NL:SB:NC:US\t0/0:34:22:23:0.043:20:-100.0000:0.0000:0,0,0,0,0,0,0,1,0,0,0,2";
string skip2 = "chr4\t169663558\t.\tT\tTGGTGAGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG\t100\tPASS\tDP=71\tGT:GQ:AD:DP:VF:NL:SB:NC:US\t0/1:32:25,46:71:0.648:20:-10.1946:0.0000:0,0,0,0,0,0,0,1,0,0,0,2";
string skip3 = "chr15\t91310151\t.\tATATCTGA\tATTAGATTC,<M>\t0\tq20;SB;LowVariantFreq;ForcedReport\tDP=34\tGT:GQ:AD:DP:VF\t2/2:10:34,0,0:34:0.000";
string skip4 = "chr4\t169663673\t.\tAT\tTG\t100\tPASS\tDP=56\tGT:GQ:AD:DP:VF:NL:SB\t1/1:100:6,50:56:0.893:20:-15.2723";
Assert.Equal(TypeOfUpdateNeeded.NoChangeNeeded, QualityRecalibration.CanSkipVcfLine(skip1));
Assert.Equal(TypeOfUpdateNeeded.NoChangeNeeded, QualityRecalibration.CanSkipVcfLine(skip2));
Assert.Equal(TypeOfUpdateNeeded.NoChangeNeeded, QualityRecalibration.CanSkipVcfLine(skip3));
Assert.Equal(TypeOfUpdateNeeded.NoChangeNeeded, QualityRecalibration.CanSkipVcfLine(skip4));
//lines we must process
string do1 = "chr4\t169663557\t.\tT\tG\t100\tPASS\tDP=23\tGT:GQ:AD:DP:VF:NL:SB:NC:US\t0/0:34:22:23:0.043:20:-100.0000:0.0000:0,0,0,0,0,0,0,1,0,0,0,2";
string do2 = "chr4\t169663558\t.\tT\tA\t100\tPASS\tDP=71\tGT:GQ:AD:DP:VF:NL:SB:NC:US\t0/1:32:25,46:71:0.648:20:-10.1946:0.0000:0,0,0,0,0,0,0,1,0,0,0,2";
string do3 = "chr15\t91310151\t.\tA\tC\t0\tq20;SB;LowVariantFreq;ForcedReport\tDP=34\tGT:GQ:AD:DP:VF\t2/2:10:34,0,0:34:0.000";
string do4 = "chr4\t169663673\t.\tA\tG\t100\tPASS\tDP=56\tGT:GQ:AD:DP:VF:NL:SB\t1/1:100:6,50:56:0.893:20:-15.2723";
Assert.Equal(TypeOfUpdateNeeded.Modify, QualityRecalibration.CanSkipVcfLine(do1));
Assert.Equal(TypeOfUpdateNeeded.Modify, QualityRecalibration.CanSkipVcfLine(do2));
Assert.Equal(TypeOfUpdateNeeded.Modify, QualityRecalibration.CanSkipVcfLine(do3));
Assert.Equal(TypeOfUpdateNeeded.Modify, QualityRecalibration.CanSkipVcfLine(do4));
}
public void TestOnADiploidVcf()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "TestWithDiploidCalls.vcf");
var countsPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Dirty.counts");
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "RecalibrateDiploidVcf");
var outFile = Path.Combine(outDir, "TestWithDiploidCalls.vcf.recal");
var expectedFile = Path.Combine(TestPaths.LocalTestDataDirectory, "ExpectedDiploidCalls.vcf.recal");
if (File.Exists(outFile))
{
File.Delete(outFile);
}
Logger.OpenLog(outDir, "RecalibrateDiploidCallsLog.txt", true);
VQROptions options = new VQROptions
{
CommandLineArguments = new string[] { "-vcf", "TestWithDiploidCalls.vcf" },
// FilterQScore = 30, <- set below
ZFactor = 0,
MaxQScore = 66,
// BaseQNoise = 30, <- set below
VcfPath = vcfPath,
OutputDirectory = outDir,
};
options.BamFilterParams.MinimumBaseCallQuality = 30; //-1
options.VariantCallingParams.MinimumVariantQScoreFilter = 30;
options.VariantCallingParams.PloidyModel = PloidyModel.DiploidByThresholding;
options.VcfWritingParams.AllowMultipleVcfLinesPerLoci = false;
options.VariantCallingParams.AmpliconBiasFilterThreshold = null;
SignatureSorterResultFiles resultFiles = new SignatureSorterResultFiles(countsPath, "foo.txt", "foo.txt");
QualityRecalibration.Recalibrate(resultFiles, options);
Logger.CloseLog();
Assert.True(File.Exists(outFile));
TestUtilities.TestHelper.CompareFiles(outFile, expectedFile);
//redirect log incase any other thread is logging here.
var SafeLogDir = TestPaths.LocalScratchDirectory;
Logger.OpenLog(SafeLogDir, "DefaultLog.txt", true);
Logger.CloseLog();
//delete our log
File.Delete(outFile);
}
public void UpdateVariant()
{
var v = SetUpCalledAllele();
var catalog = new Dictionary <MutationCategory, int>();
catalog.Add(MutationCategory.CtoA, 12);
Assert.Equal(666, v.VariantQscore);
QualityRecalibration.UpdateVariantQScoreAndRefilter(100, 5, catalog, v, MutationCategory.CtoA, false);
Assert.Equal(12, v.NoiseLevelApplied);
Assert.Equal(10, v.GenotypeQscore);
Assert.Equal(10, v.VariantQscore);
Assert.Equal(0, v.Filters.Count);
v.VariantQscore = 666;
QualityRecalibration.UpdateVariantQScoreAndRefilter(100, 30, catalog, v, MutationCategory.CtoA, false);
Assert.Equal(10, v.VariantQscore);
Assert.Equal(1, v.Filters.Count);
Assert.Equal(FilterType.LowVariantQscore, v.Filters[0]);
v.VariantQscore = 666;
v.Filters.Add(FilterType.OffTarget);//any filter will do to test, that isnt the q30 one.
QualityRecalibration.UpdateVariantQScoreAndRefilter(100, 30, catalog, v, MutationCategory.CtoA, false);
Assert.Equal(10, v.VariantQscore);
Assert.Equal(2, v.Filters.Count);
Assert.Equal(FilterType.LowVariantQscore, v.Filters[0]);
Assert.Equal(FilterType.OffTarget, v.Filters[1]);
v.VariantQscore = 666;
v.Filters = new List <FilterType>()
{
FilterType.LowVariantQscore
};
QualityRecalibration.UpdateVariantQScoreAndRefilter(100, 30, catalog, v, MutationCategory.CtoA, false);
Assert.Equal(10, v.VariantQscore);
Assert.Equal(1, v.Filters.Count);
Assert.Equal(FilterType.LowVariantQscore, v.Filters[0]);
v.VariantQscore = 666;
v.Filters = new List <FilterType>()
{
FilterType.LowVariantQscore, FilterType.OffTarget
};
QualityRecalibration.UpdateVariantQScoreAndRefilter(100, 30, catalog, v, MutationCategory.CtoA, false);
Assert.Equal(10, v.VariantQscore);
Assert.Equal(FilterType.LowVariantQscore, v.Filters[0]);
Assert.Equal(FilterType.OffTarget, v.Filters[1]);
}
public void HaveInfoToUpdateQ()
{
var v = SetUpCalledAllele(); //(by default, this is reference type)
double depth;
double callCount;
Assert.Equal(true, QualityRecalibration.HaveInfoToUpdateQ(v, out depth, out callCount));
v.Type = AlleleCategory.Unsupported;
Assert.Equal(false, QualityRecalibration.HaveInfoToUpdateQ(v, out depth, out callCount));
v.Type = AlleleCategory.Deletion;
Assert.Equal(true, QualityRecalibration.HaveInfoToUpdateQ(v, out depth, out callCount));
Assert.Equal(100, depth);
Assert.Equal(10, callCount);
}
public void InsertNewQ()
{
var v = SetUpCalledAllele();
Assert.Equal(20, v.NoiseLevelApplied);
Assert.Equal(72, v.GenotypeQscore);
Assert.Equal(666, v.VariantQscore);
var catalog = new Dictionary <MutationCategory, int>();
catalog.Add(MutationCategory.CtoA, 12);
QualityRecalibration.InsertNewQ(catalog, v, MutationCategory.CtoA, 42, true);
Assert.Equal(12, v.NoiseLevelApplied);
Assert.Equal(42, v.GenotypeQscore);
Assert.Equal(42, v.VariantQscore);
}
public void RecalibrateCleanVcf()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Test.vcf");
var countsPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Clean.counts");
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "RecalibrateDirtyVcf");
var outFile = Path.Combine(outDir, "Test.vcf.recal");
var expectedFile = Path.Combine(TestPaths.LocalTestDataDirectory, "ExpectedTest.vcf.recal");
if (File.Exists(outFile))
{
File.Delete(outFile);
}
Logger.OpenLog(TestPaths.LocalScratchDirectory, "RecalibrateCleanVcfLog.txt", true);
VQROptions options = new VQROptions
{
CommandLineArguments = null,
// FilterQScore = -1,
ZFactor = 0,
MaxQScore = 66,
// BaseQNoise = 30,
OutputDirectory = outDir
};
options.VariantCallingParams.MinimumVariantQScoreFilter = -1;
options.BamFilterParams.MinimumBaseCallQuality = 30;
SignatureSorterResultFiles resultFiles = new SignatureSorterResultFiles(countsPath, "foo.txt", "foo.txt");
QualityRecalibration.Recalibrate(resultFiles, options);
Logger.CloseLog();
//no recalibration should occur for a clean file.
Assert.True(!File.Exists(outFile));
//redirect log incase any other thread is logging here.
var SafeLogDir = TestPaths.LocalScratchDirectory;
Logger.OpenLog(SafeLogDir, "DefaultLog.txt", true);
Logger.CloseLog();
}
public void InsertNewQ()
{
var v = SetUpVariant();
Assert.Equal("20", v.Genotypes[0]["NL"]);
Assert.Equal("72", v.Genotypes[0]["GQ"]);
Assert.Equal("34", v.Genotypes[0]["GQX"]);
Assert.Equal(666, v.Quality);
var catalog = new Dictionary <MutationCategory, int>();
catalog.Add(MutationCategory.CtoA, 12);
QualityRecalibration.InsertNewQ(catalog, v, MutationCategory.CtoA, 42);
Assert.Equal("12", v.Genotypes[0]["NL"]);
Assert.Equal("42", v.Genotypes[0]["GQ"]);
Assert.Equal("42", v.Genotypes[0]["GQX"]);
Assert.Equal(42, v.Quality);
}
public void UpdateVariant()
{
var v = SetUpVariant();
var catalog = new Dictionary <MutationCategory, int>();
catalog.Add(MutationCategory.CtoA, 12);
Assert.Equal(666, v.Quality);
QualityRecalibration.UpdateVariant(100, 5, catalog, v, MutationCategory.CtoA);
Assert.Equal("12", v.Genotypes[0]["NL"]);
Assert.Equal("10", v.Genotypes[0]["GQ"]);
Assert.Equal("10", v.Genotypes[0]["GQX"]);
Assert.Equal(10, v.Quality);
Assert.Equal("PASS", v.Filters);
v.Quality = 666;
QualityRecalibration.UpdateVariant(100, 30, catalog, v, MutationCategory.CtoA);
Assert.Equal(10, v.Quality);
Assert.Equal("q30", v.Filters);
v.Quality = 666;
v.Filters = "Snoopy";
QualityRecalibration.UpdateVariant(100, 30, catalog, v, MutationCategory.CtoA);
Assert.Equal(10, v.Quality);
Assert.Equal("Snoopy;q30", v.Filters);
v.Quality = 666;
v.Filters = "q30";
QualityRecalibration.UpdateVariant(100, 30, catalog, v, MutationCategory.CtoA);
Assert.Equal(10, v.Quality);
Assert.Equal("q30", v.Filters);
v.Quality = 666;
v.Filters = "Snoopy;q30";
QualityRecalibration.UpdateVariant(100, 30, catalog, v, MutationCategory.CtoA);
Assert.Equal(10, v.Quality);
Assert.Equal("Snoopy;q30", v.Filters);
}
public void HaveInfoToUpdateQ()
{
var v = new VcfVariant();
int depth;
int callCount;
Assert.Equal(false, QualityRecalibration.HaveInfoToUpdateQ(v, out depth, out callCount));
v.Genotypes = new List <Dictionary <string, string> >()
{
new Dictionary <string, string>()
};
v.InfoFields = new Dictionary <string, string>();
v.InfoFields.Add("PX", "42");
v.Genotypes[0].Add("blah", "??");
Assert.Equal(false, QualityRecalibration.HaveInfoToUpdateQ(v, out depth, out callCount));
v.InfoFields.Add("DP", "100");
v.Genotypes[0].Add("AD", "90,10");
Assert.Equal(true, QualityRecalibration.HaveInfoToUpdateQ(v, out depth, out callCount));
Assert.Equal(100, depth);
Assert.Equal(10, callCount);
}