Examples with Target org.broadinstitute.hellbender.tools.exome.Target used on opensource projects

Example 51 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class XHMMSegmentCallerIntegrationTest method testRunCommandLine.

//TODO: this test used to contain a test of concordance with XHMM.  It no longer does that because our model has
//TODO: diverged from XHMM's.  Eventually the right thing to do is use the simulateChain() method to generate
//TODO: simulated data for some artificial set of CNV segments and to test concordance with those segments.
//TODO: however we still use XHMM's emission model, which is both not generative and quite silly.  Once we
//TODO: have a generative model of coverage we can modify simulateChain() accordingly and then write a concordance
//TODO: test here.  Until then, we do not have an integration test but we do have our ongoing evaluations, which
//TODO: show the superiority of our modifications versus the original XHMM model.
@Test(dataProvider = "simulatedChainData")
public File testRunCommandLine(final XHMMData chain) {
    final File inputFile = writeChainInTempFile(chain);
    final File outputFile = createTempFile("output", ".tab");
    runCommandLine(chain, inputFile, outputFile);
    Assert.assertTrue(outputFile.exists());
    final TargetCollection<Target> targets = TargetArgumentCollection.readTargetCollection(REALISTIC_TARGETS_FILE);
    final List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> outputRecords = readOutputRecords(outputFile);
    assertOutputIsInOrder(outputRecords, targets);
    assertOutputHasConsistentNumberOfTargets(outputRecords, targets);
    final Map<String, List<HiddenStateSegmentRecord<CopyNumberTriState, Target>>> outputRecordsBySample = splitOutputRecordBySample(outputRecords);
    assertSampleNames(outputRecordsBySample.keySet(), chain);
    for (final List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> sampleRecords : outputRecordsBySample.values()) {
        assertSampleSegmentsCoverAllTargets(sampleRecords, targets);
        assertSampleSegmentsCoordinates(sampleRecords, targets);
    }
    return outputFile;
}

Example 52 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class XHMMSegmentCallerIntegrationTest method assertOutputHasConsistentNumberOfTargets.

private void assertOutputHasConsistentNumberOfTargets(final List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> outputRecords, final TargetCollection<Target> targets) {
    for (final HiddenStateSegmentRecord<CopyNumberTriState, Target> nextRecord : outputRecords) {
        final IndexRange indexRange = targets.indexRange(nextRecord.getSegment());
        Assert.assertEquals(indexRange.to - indexRange.from, nextRecord.getSegment().getTargetCount());
    }
}

Example 53 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class XHMMSegmentCallerIntegrationTest method assertSampleSegmentsCoverAllTargets.

private void assertSampleSegmentsCoverAllTargets(final List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> sampleRecords, final TargetCollection<Target> targets) {
    int next = 0;
    for (final HiddenStateSegmentRecord<CopyNumberTriState, Target> record : sampleRecords) {
        final IndexRange range = targets.indexRange(record.getSegment());
        Assert.assertEquals(range.from, next);
        next = range.to;
    }
}

Example 54 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class XHMMSegmentCallerIntegrationTest method assertOutputIsInOrder.

private void assertOutputIsInOrder(final List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> outputRecords, final TargetCollection<Target> targets) {
    for (int i = 1; i < outputRecords.size(); i++) {
        final HiddenStateSegmentRecord<CopyNumberTriState, Target> nextRecord = outputRecords.get(i);
        final HiddenStateSegmentRecord<CopyNumberTriState, Target> previousRecord = outputRecords.get(i - 1);
        final IndexRange nextRange = targets.indexRange(nextRecord.getSegment());
        final IndexRange previousRange = targets.indexRange(previousRecord.getSegment());
        Assert.assertTrue(nextRange.from >= previousRange.from);
    }
}

Example 55 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk by broadinstitute.

the class XHMMSegmentCallerIntegrationTest method assertSampleSegmentsCoordinates.

private void assertSampleSegmentsCoordinates(List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> sampleRecords, TargetCollection<Target> targets) {
    for (final HiddenStateSegmentRecord<CopyNumberTriState, Target> record : sampleRecords) {
        final IndexRange range = targets.indexRange(record.getSegment());
        Assert.assertTrue(range.size() > 0);
        Assert.assertEquals(record.getSegment().getContig(), targets.location(range.from).getContig());
        Assert.assertEquals(record.getSegment().getStart(), targets.location(range.from).getStart());
        Assert.assertEquals(record.getSegment().getEnd(), targets.location(range.to - 1).getEnd());
    }
}