public void WriteCountsFile()
{
VQROptions options = new VQROptions()
{
VcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "TestSignatureSorter.vcf"),
OutputDirectory = TestPaths.LocalScratchDirectory,
LociCount = -1,
DoBasicChecks = true,
DoAmpliconPositionChecks = false
};
var expectedPath = Path.Combine(TestPaths.LocalTestDataDirectory, "Expected.counts");
SignatureSorterResultFiles results = SignatureSorter.StrainVcf(options);
string outFile = results.BasicCountsFilePath;
Assert.True(File.Exists(outFile));
var observedLines = File.ReadAllLines(outFile);
var expectedLines = File.ReadAllLines(expectedPath);
Assert.Equal(expectedLines.Length, observedLines.Length);
for (int i = 0; i < expectedLines.Length; i++)
{
Assert.Equal(expectedLines[i], observedLines[i]);
}
File.Delete(outFile);
}
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 WriteEdgeCountsFile()
{
/*
* chr10 7577500.C G //on edge (within 2 bases of chr10 amplicon end)
* chr10 7577501.C G //on edge (within 2 bases of chr10 amplicon end)
* chr17 7577537.C G 100 PASS DP = 10 //on edge (within 2 bases of chr17 amplicon start)
* chr17 7577538.C G 100 PASS DP = 11 //on edge (within 2 bases of chr17 amplicon start)
* chr17 7577540.G A 100 PASS DP = 13 //NOT on edge
* chr17 7577541.T A 100 PASS DP = 100 //on edge (within 2 bases of edge of hat distribution)
* chr17 7577542.G T 100 PASS DP = 101 //on edge (within 2 bases of edge of hat distribution)
* chr17 7577543.T C 100 PASS DP = 100 //on edge (within 2 bases of edge of hat distribution)
* chr17 7577544.T C 100 PASS DP = 56 //on edge (within 2 bases of edge of hat distribution)
* chr17 7577549.C. 100 PASS DP = 10 //NOT on edge
* chr17 7577550.C. 100 PASS DP = 10 //NOT on edge
* chr17 7577552.C A 100 PASS DP = 15 //NOT on edge
* chr17 7577553.T C 100 PASS DP = 16 //on edge (within 2 bases of edge of hat distribution)
* chr17 7577554.C. 100 PASS DP = 3700 //on edge (within 2 bases of edge of hat distribution), BUT its a referece call so we dont count it
* chr17 7577555.C. 100 PASS DP = 0 //NOT on edge (DP=0)
* chr17 7577556.C A 100 PASS DP = 0 //NOT on edge (DP=0)
* chr17 7577557.C A 100 PASS DP = 0 //NOT on edge (DP=0)
* chr17 7577558.C A 100 PASS DP = 0 //NOT on edge (DP=0)
* chr20 7577554.C G 100 PASS DP = 3700 //on edge (within 2 bases of edge of hat distribution)
* chr20 7577555.C. 100 PASS DP = 0 //NOT on edge (DP=0)
*/
VQROptions options = new VQROptions()
{
VcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "FindEdges.vcf"),
OutputDirectory = Path.Combine(TestPaths.LocalScratchDirectory, "WriteEdgeCountsFile"),
LociCount = -1,
DoBasicChecks = false,
DoAmpliconPositionChecks = true,
ExtentofEdgeRegion = 2
};
var expectedCountsFile = Path.Combine(TestPaths.LocalTestDataDirectory, "Expected.edgecounts");
var expectedIssuesFile = Path.Combine(TestPaths.LocalTestDataDirectory, "Expected.edgevariants");
TestUtilities.TestHelper.RecreateDirectory(options.OutputDirectory);
SignatureSorterResultFiles results = SignatureSorter.StrainVcf(options);
TestUtilities.TestHelper.CompareFiles(results.AmpliconEdgeCountsFilePath, expectedCountsFile);
TestUtilities.TestHelper.CompareFiles(results.AmpliconEdgeSuspectListFilePath, expectedIssuesFile);
TestUtilities.TestHelper.RecreateDirectory(options.OutputDirectory);
}
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 WriteEdgeCountsFileGivenLociCounts()
{
VQROptions options = new VQROptions()
{
VcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "FindEdges.vcf"),
OutputDirectory = Path.Combine(TestPaths.LocalScratchDirectory, "WriteEdgeCountsFileGivenLociCounts"),
LociCount = 1000,
DoBasicChecks = false,
DoAmpliconPositionChecks = true,
ExtentofEdgeRegion = 2
};
var expectedPath = Path.Combine(TestPaths.LocalTestDataDirectory, "ExpectedGivenLociNum.edgecounts");
TestUtilities.TestHelper.RecreateDirectory(options.OutputDirectory);
SignatureSorterResultFiles results = SignatureSorter.StrainVcf(options);
string outFile = results.AmpliconEdgeCountsFilePath;
TestUtilities.TestHelper.CompareFiles(results.AmpliconEdgeCountsFilePath, expectedPath);
TestUtilities.TestHelper.RecreateDirectory(options.OutputDirectory);
}
