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

Example 91 with IntegrationTestSpec

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

the class ExampleFeatureWalkerIntegrationTest method testExampleFeatureWalkerWithIntervals.

@Test
public void testExampleFeatureWalkerWithIntervals() throws IOException {
    IntegrationTestSpec testSpec = new IntegrationTestSpec(" -R " + hg19MiniReference + " -I " + TEST_DATA_DIRECTORY + "reads_data_source_test1.bam" + " -F " + TEST_DATA_DIRECTORY + "example_features.bed" + " -L 1 " + " -auxiliaryVariants " + TEST_DATA_DIRECTORY + "feature_data_source_test.vcf" + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expected_ExampleFeatureWalkerIntegrationTestWithIntervals_output.txt"));
    testSpec.executeTest("testExampleIntervalWalker", this);
}

Example 92 with IntegrationTestSpec

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

the class ExampleIntervalWalkerIntegrationTest method testExampleIntervalWalker.

@Test
public void testExampleIntervalWalker() throws IOException {
    IntegrationTestSpec testSpec = new IntegrationTestSpec(" -L 1:100-200 -L 2:500-600" + " -R " + hg19MiniReference + " -I " + TEST_DATA_DIRECTORY + "reads_data_source_test1.bam" + " -V " + TEST_DATA_DIRECTORY + "feature_data_source_test.vcf" + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expected_ExampleIntervalWalkerIntegrationTest_output.txt"));
    testSpec.executeTest("testExampleIntervalWalker", this);
}

Example 93 with IntegrationTestSpec

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

the class ExampleLocusWalkerIntegrationTest method testExampleVariantWalker.

@Test
public void testExampleVariantWalker() throws IOException {
    IntegrationTestSpec testSpec = new IntegrationTestSpec(" -L 1" + " -R " + hg19MiniReference + " -I " + TEST_DATA_DIRECTORY + "reads_data_source_test1.bam" + " -V " + TEST_DATA_DIRECTORY + "feature_data_source_test.vcf" + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expected_ExampleLocusWalkerIntegrationTest_output.txt"));
    testSpec.executeTest("testExampleLocusWalker", this);
}

Example 94 with IntegrationTestSpec

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

the class ExampleReadWalkerWithReferenceIntegrationTest method testExampleVariantWalker.

@Test
public void testExampleVariantWalker() throws IOException {
    final IntegrationTestSpec testSpec = new IntegrationTestSpec(" -R " + hg19MiniReference + " -I " + TEST_DATA_DIRECTORY + "reads_data_source_test1.bam" + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expected_ExampleReadWalkerWithReferenceIntegrationTest_output.txt"));
    testSpec.executeTest("testExampleReadWalkerWithReference", this);
}

Example 95 with IntegrationTestSpec

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

the class CalculateGenotypePosteriorsIntegrationTest method testInputINDELs.

@Test
public void testInputINDELs() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec("-useACoff" + " -O %s" + " -R " + //NOTE: we need a reference for -L
    b37_reference_20_21 + " -L 20:10,000,000-10,100,000" + " -V " + dir + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" + " -supporting " + largeDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf" + " -addOutputVCFCommandLine false", Collections.singletonList(dir + "expectedCGP_testInputINDELs.vcf"));
    spec.executeTest("testInputINDELs", this);
}