Examples with IntegrationTestSpec org.broadinstitute.hellbender.utils.test.IntegrationTestSpec used on opensource projects

Example 76 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class VariantFiltrationIntegrationTest method testInvertGenotypeFilterExpression.

@Test
public void testInvertGenotypeFilterExpression() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString("filteringDepthInFormat.vcf", " --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP --invertGenotypeFilterExpression "), Arrays.asList(getToolTestDataDir() + "expected/" + "testVariantFiltration_testInvertGenotypeFilterExpression.vcf"));
    spec.executeTest("testInvertGenotypeFilterExpression", this);
}

Example 77 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class VariantFiltrationIntegrationTest method testFilterWithSeparateNames.

@Test
public void testFilterWithSeparateNames() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString("vcfexample2.vcf", " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' "), Arrays.asList(getToolTestDataDir() + "expected/" + "testVariantFiltration_testFilterWithSeparateNames.vcf"));
    spec.executeTest("testFilterWithSeparateNames", this);
}

Example 78 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class VariantFiltrationIntegrationTest method testDeletions.

@Test
public void testDeletions() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString("twoDeletions.vcf", " --filterExpression 'QUAL < 100' --filterName foo "), Arrays.asList(getToolTestDataDir() + "expected/" + "testVariantFiltration_testDeletions.vcf"));
    spec.executeTest("testDeletions", this);
}

Example 79 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class VariantFiltrationIntegrationTest method testSetFilteredGtoNocall.

@Test
public void testSetFilteredGtoNocall() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString("filteringDepthInFormat.vcf", " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP --setFilteredGtToNocall "), Arrays.asList(getToolTestDataDir() + "expected/" + "testVariantFiltration_testSetFilteredGtoNocall.vcf"));
    spec.executeTest("testSetFilteredGtoNocall", this);
}

Example 80 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class VariantFiltrationIntegrationTest method testGenotypeFilters2.

@Test
public void testGenotypeFilters2() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString("vcfexample2.vcf", " -G_filter 'isHomVar == 1' -G_filterName foo "), Arrays.asList(getToolTestDataDir() + "expected/" + "testVariantFiltration_testGenotypeFilters2.vcf"));
    spec.executeTest("testGenotypeFilters2", this);
}