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 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 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 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 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();
}