public void RewriteSpecialDeletionTest()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "DeletionSpecialCaseTest.vcf");
var expectedPath = Path.Combine(TestPaths.LocalTestDataDirectory, "DeletionSpecialCaseTest.recal.vcf");
var outPath = TestPaths.LocalScratchDirectory;
var options = new AdaptiveGtOptions
{
VcfPath = vcfPath
};
AdaptiveGtWriter.RewriteVcf(vcfPath, outPath, options, DefaultResults);
string outFile = Path.Combine(outPath, "DeletionSpecialCaseTest.recal.vcf");
Assert.True(File.Exists(outFile));
CompareVariants.AssertSameVariants_QScoreAgnostic(outFile, expectedPath);
File.Delete(outFile);
}
public void RecalibrateTest()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "testData.PairRealigned.genome.vcf");
var expectedPath = Path.Combine(TestPaths.LocalTestDataDirectory, "testData.PairRealigned.genome.model");
var vcfOutTestFile = Path.Combine(TestPaths.LocalTestDataDirectory, "testData.PairRealigned.recal.vcf");
var outPath = TestPaths.LocalScratchDirectory;
var vcfOutFile = Path.Combine(outPath, "testData.PairRealigned.recal.vcf");
var options = new AdaptiveGtOptions
{
VcfPath = vcfPath,
OutputDirectory = outPath
};
Recalibration recal = new Recalibration(options);
recal.Recalibrate();
// Check model file
var outFile = Path.Combine(outPath, "testData.PairRealigned.genome.model");
TestHelper.CompareFiles(outFile, expectedPath);
// Check vcf file
Assert.True(File.Exists(vcfOutFile));
CompareVariants.AssertSameVariants_QScoreAgnostic(vcfOutFile, vcfOutTestFile);
File.Delete(vcfOutFile);
// Use model to generate vcf and check file
recal = new Recalibration(options);
recal.Recalibrate();
Assert.True(File.Exists(vcfOutFile));
CompareVariants.AssertSameVariants_QScoreAgnostic(vcfOutFile, vcfOutTestFile);
File.Delete(outFile);
File.Delete(vcfOutFile);
}
