use of org.broadinstitute.hellbender.tools.exome.pulldown.Pulldown in project gatk-protected by broadinstitute.
the class GetBayesianHetCoverageIntegrationTest method testNormalJob.
@Test
public void testNormalJob() {
final File normalOutputFile = createTempFile("normal-test", ".tsv");
Pulldown normalHetPulldownExpected, normalHetPulldownResult;
/* test 1: tight calling stringency */
final String[] args_1 = { "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REF_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.SNP_FILE_SHORT_NAME, SNP_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.NORMAL_BAM_FILE_SHORT_NAME, NORMAL_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME, normalOutputFile.getAbsolutePath(), "-" + GetBayesianHetCoverage.READ_DEPTH_THRESHOLD_SHORT_NAME, Integer.toString(10), "-" + GetBayesianHetCoverage.HET_CALLING_STRINGENCY_SHORT_NAME, Double.toString(15.0) };
runCommandLine(args_1);
normalHetPulldownExpected = new Pulldown(normalHeader);
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 14630, 14630), 9, 8, Nucleotide.T, Nucleotide.G, 17, 39.99));
normalHetPulldownResult = new Pulldown(normalOutputFile, normalHeader);
Assert.assertEquals(normalHetPulldownExpected, normalHetPulldownResult);
/* test 2: loose calling stringency */
final String[] args_2 = { "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REF_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.SNP_FILE_SHORT_NAME, SNP_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.NORMAL_BAM_FILE_SHORT_NAME, NORMAL_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME, normalOutputFile.getAbsolutePath(), "-" + GetBayesianHetCoverage.READ_DEPTH_THRESHOLD_SHORT_NAME, Integer.toString(10), "-" + GetBayesianHetCoverage.HET_CALLING_STRINGENCY_SHORT_NAME, Double.toString(2.0) };
runCommandLine(args_2);
normalHetPulldownExpected = new Pulldown(normalHeader);
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 11522, 11522), 7, 4, Nucleotide.G, Nucleotide.A, 11, 18.60));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 12098, 12098), 8, 6, Nucleotide.G, Nucleotide.T, 14, 29.29));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 14630, 14630), 9, 8, Nucleotide.T, Nucleotide.G, 17, 39.99));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14689, 14689), 6, 9, Nucleotide.T, Nucleotide.G, 15, 28.60));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14982, 14982), 6, 5, Nucleotide.G, Nucleotide.C, 11, 24.99));
normalHetPulldownResult = new Pulldown(normalOutputFile, normalHeader);
Assert.assertEquals(normalHetPulldownExpected, normalHetPulldownResult);
}
use of org.broadinstitute.hellbender.tools.exome.pulldown.Pulldown in project gatk-protected by broadinstitute.
the class GetHetCoverageIntegrationTest method testGetHetCoverageNormalOnly.
@Test
public void testGetHetCoverageNormalOnly() {
final String[] arguments = { "-" + ExomeStandardArgumentDefinitions.NORMAL_BAM_FILE_SHORT_NAME, NORMAL_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.SNP_FILE_SHORT_NAME, SNP_FILE.getAbsolutePath(), "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REF_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME, normalOutputFile.getAbsolutePath(), // Non-default value of 10, since test data was calculated with 10
"-" + GetHetCoverage.MINIMUM_READ_COUNT_FULL_NAME, Integer.toString(10) };
runCommandLine(arguments);
final Pulldown normalOutputPulldownResult = new Pulldown(normalOutputFile, normalHeader);
Assert.assertEquals(normalHetPulldownExpected, normalOutputPulldownResult);
}
use of org.broadinstitute.hellbender.tools.exome.pulldown.Pulldown in project gatk-protected by broadinstitute.
the class GetHetCoverageIntegrationTest method initHeaders.
@BeforeClass
public void initHeaders() throws IOException {
try (final SamReader normalBamReader = SamReaderFactory.makeDefault().open(NORMAL_BAM_FILE);
final SamReader tumorBamReader = SamReaderFactory.makeDefault().open(TUMOR_BAM_FILE)) {
normalHeader = normalBamReader.getFileHeader();
tumorHeader = tumorBamReader.getFileHeader();
normalHetPulldownExpected = new Pulldown(normalHeader);
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 11522, 11522), 7, 4));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 12098, 12098), 8, 6));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 14630, 14630), 9, 8));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14689, 14689), 6, 9));
normalHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14982, 14982), 6, 5));
tumorHetPulldownExpected = new Pulldown(tumorHeader);
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 11522, 11522), 7, 4));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 12098, 12098), 8, 6));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 14630, 14630), 9, 8));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14689, 14689), 6, 9));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14982, 14982), 6, 5));
}
}
use of org.broadinstitute.hellbender.tools.exome.pulldown.Pulldown in project gatk-protected by broadinstitute.
the class GetBayesianHetCoverageIntegrationTest method testTumorJob.
@Test
public void testTumorJob() {
final File tumorOutputFile = createTempFile("tumor-test", ".tsv");
Pulldown tumorHetPulldownExpected, tumorHetPulldownResult;
/* test 1: tight calling stringency */
final String[] args_1 = { "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REF_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.SNP_FILE_SHORT_NAME, SNP_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.TUMOR_BAM_FILE_SHORT_NAME, TUMOR_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME, tumorOutputFile.getAbsolutePath(), "-" + GetBayesianHetCoverage.READ_DEPTH_THRESHOLD_SHORT_NAME, Integer.toString(10), "-" + GetBayesianHetCoverage.HET_CALLING_STRINGENCY_SHORT_NAME, Double.toString(10.0) };
runCommandLine(args_1);
tumorHetPulldownExpected = new Pulldown(tumorHeader);
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 12098, 12098), 8, 6, Nucleotide.G, Nucleotide.T, 14, 24.85));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 14630, 14630), 9, 8, Nucleotide.T, Nucleotide.G, 17, 34.03));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14689, 14689), 6, 9, Nucleotide.T, Nucleotide.G, 15, 24.23));
tumorHetPulldownResult = new Pulldown(tumorOutputFile, tumorHeader);
Assert.assertEquals(tumorHetPulldownExpected, tumorHetPulldownResult);
/* test 2: tight calling stringency */
final String[] args_2 = { "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REF_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.SNP_FILE_SHORT_NAME, SNP_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.TUMOR_BAM_FILE_SHORT_NAME, TUMOR_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME, tumorOutputFile.getAbsolutePath(), "-" + GetBayesianHetCoverage.READ_DEPTH_THRESHOLD_SHORT_NAME, Integer.toString(10), "-" + GetBayesianHetCoverage.HET_CALLING_STRINGENCY_SHORT_NAME, Double.toString(5.0) };
runCommandLine(args_2);
tumorHetPulldownExpected = new Pulldown(tumorHeader);
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 11522, 11522), 7, 4, Nucleotide.G, Nucleotide.A, 11, 15.72));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 12098, 12098), 8, 6, Nucleotide.G, Nucleotide.T, 14, 24.85));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("1", 14630, 14630), 9, 8, Nucleotide.T, Nucleotide.G, 17, 34.03));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14689, 14689), 6, 9, Nucleotide.T, Nucleotide.G, 15, 24.23));
tumorHetPulldownExpected.add(new AllelicCount(new SimpleInterval("2", 14982, 14982), 6, 5, Nucleotide.G, Nucleotide.C, 11, 21.23));
tumorHetPulldownResult = new Pulldown(tumorOutputFile, tumorHeader);
Assert.assertEquals(tumorHetPulldownExpected, tumorHetPulldownResult);
}
use of org.broadinstitute.hellbender.tools.exome.pulldown.Pulldown in project gatk-protected by broadinstitute.
the class GetHetCoverageIntegrationTest method testGetHetCoverage.
@Test
public void testGetHetCoverage() {
final String[] arguments = { "-" + ExomeStandardArgumentDefinitions.NORMAL_BAM_FILE_SHORT_NAME, NORMAL_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.TUMOR_BAM_FILE_SHORT_NAME, TUMOR_BAM_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.SNP_FILE_SHORT_NAME, SNP_FILE.getAbsolutePath(), "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REF_FILE.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.NORMAL_ALLELIC_COUNTS_FILE_SHORT_NAME, normalOutputFile.getAbsolutePath(), "-" + ExomeStandardArgumentDefinitions.TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME, tumorOutputFile.getAbsolutePath(), // Non-default value of 10, since test data was calculated with 10
"-" + GetHetCoverage.MINIMUM_READ_COUNT_FULL_NAME, Integer.toString(10) };
runCommandLine(arguments);
final Pulldown normalOutputPulldownResult = new Pulldown(normalOutputFile, normalHeader);
final Pulldown tumorOutputPulldownResult = new Pulldown(tumorOutputFile, tumorHeader);
Assert.assertEquals(normalHetPulldownExpected, normalOutputPulldownResult);
Assert.assertEquals(tumorHetPulldownExpected, tumorOutputPulldownResult);
}
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