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); }