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

Example 56 with IntegrationTestSpec

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

the class PileupIntegrationTest method testInsertLengthPileup.

@Test
public void testInsertLengthPileup() throws Exception {
    // GATK 3.5 code have a the last line with a REDUCE RESULT that was removed in this implementation
    IntegrationTestSpec testSpec = new IntegrationTestSpec(" -L 20:10000092-10000112" + " -R " + b37_reference_20_21 + " -I " + NA12878_20_21_WGS_bam + " -outputInsertLength " + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expectedInsertLengthPileup.txt"));
    testSpec.executeTest("testInsertLengthPileup", this);
}

Example 57 with IntegrationTestSpec

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

the class SplitNCigarReadsIntegrationTest method testSplitsOfUnpairedAndUnmappedReads.

//regression test for https://github.com/broadinstitute/gatk/pull/1853
@Test
public void testSplitsOfUnpairedAndUnmappedReads() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R" + b37_reference_20_21 + " -I " + largeFileTestDir + "K-562.duplicateMarked.chr20.bam -O %s --processSecondaryAlignments", Arrays.asList(largeFileTestDir + "expected.K-562.splitNCigarReads.chr20.bam"));
    spec.executeTest("regression test for unmapped and unpaired reads", this);
}

Example 58 with IntegrationTestSpec

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

the class SplitNCigarReadsIntegrationTest method testSplitsTargetRegionFunctionality.

//regression test for https://github.com/broadinstitute/gatk/pull/1864
@Test
public void testSplitsTargetRegionFunctionality() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R" + b37_reference_20_21 + " -I " + largeFileTestDir + "NA12878.RNAseq.bam -O %s -L 20:2444518-2454410 --processSecondaryAlignments", Arrays.asList(largeFileTestDir + "expected.NA12878.RNAseq.splitNcigarReads.subSequenceTest.bam"));
    spec.executeTest("regression test for unmapped and unpaired reads", this);
}

Example 59 with IntegrationTestSpec

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

the class SplitNCigarReadsIntegrationTest method testSplitsWithOverhangsNotClipping.

@Test
public void testSplitsWithOverhangsNotClipping() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("--doNotFixOverhangs -R " + b37_reference_20_21 + " -I " + largeFileTestDir + "NA12878.RNAseq.bam -O %s --processSecondaryAlignments", Arrays.asList(largeFileTestDir + "expected.NA12878.RNAseq.splitNcigarReads.doNotFixOverhangs.bam"));
    spec.executeTest("test splits with overhangs not clipping", this);
}

Example 60 with IntegrationTestSpec

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

the class SplitNCigarReadsIntegrationTest method testSplitsFixNDN.

@Test
public void testSplitsFixNDN() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R " + b37_reference_20_21 + " -I " + getTestDataDir() + "/" + "splitNCigarReadsSnippet.bam -O %s -fixNDN --processSecondaryAlignments", Arrays.asList(getTestDataDir() + "/" + "expected.splitNCigarReadsSnippet.splitNcigarReads.fixNDN.bam"));
    spec.executeTest("test fix NDN", this);
}