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); }