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

Example 61 with Target

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

the class SparkGenomeReadCountsIntegrationTest method testSparkGenomeReadCounts.

@Test
public void testSparkGenomeReadCounts() throws IOException {
    final File outputFile = createTempFile(BAM_FILE.getName(), ".cov");
    final String[] arguments = { "--disableSequenceDictionaryValidation", "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REFERENCE_FILE.getAbsolutePath(), "-" + StandardArgumentDefinitions.INPUT_SHORT_NAME, BAM_FILE.getAbsolutePath(), "-" + SparkGenomeReadCounts.OUTPUT_FILE_SHORT_NAME, outputFile.getAbsolutePath(), "-" + SparkGenomeReadCounts.BINSIZE_SHORT_NAME, "10000" };
    runCommandLine(arguments);
    Assert.assertTrue(outputFile.exists());
    Assert.assertTrue(outputFile.length() > 0);
    final ReadCountCollection coverage = ReadCountCollectionUtils.parse(outputFile);
    final File targetsFile = new File(outputFile.getAbsolutePath() + ".targets.tsv");
    Assert.assertTrue(targetsFile.exists());
    Assert.assertTrue(targetsFile.length() > 0);
    final List<Target> targets = TargetTableReader.readTargetFile(targetsFile);
    Assert.assertEquals(targets.size(), 8);
    Assert.assertEquals(targets.get(1).getEnd(), 16000);
    Assert.assertEquals(targets.get(5).getName(), "target_3_10001_16000");
    Assert.assertEquals(coverage.targets().size(), targets.size());
}

Example 62 with Target

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

the class SparkGenomeReadCountsIntegrationTest method testSparkGenomeReadCountsInterval.

@Test
public void testSparkGenomeReadCountsInterval() {
    final File outputFile = createTempFile(BAM_FILE.getName(), ".cov");
    final String[] arguments = { "--disableSequenceDictionaryValidation", "-" + StandardArgumentDefinitions.REFERENCE_SHORT_NAME, REFERENCE_FILE.getAbsolutePath(), "-" + StandardArgumentDefinitions.INPUT_SHORT_NAME, BAM_FILE.getAbsolutePath(), "-" + SparkGenomeReadCounts.OUTPUT_FILE_SHORT_NAME, outputFile.getAbsolutePath(), "-" + SparkGenomeReadCounts.BINSIZE_SHORT_NAME, "10000", "-L", "1" };
    runCommandLine(arguments);
    final ReadCountCollection proportionalCoverage = loadReadCountCollection(outputFile);
    Assert.assertTrue(proportionalCoverage.records().stream().noneMatch(t -> t.getContig().equals("2") || t.getContig().equals("3")));
    // raw coverage
    final ReadCountCollection rawCoverage = loadReadCountCollection(new File(outputFile.getAbsolutePath() + SparkGenomeReadCounts.RAW_COV_OUTPUT_EXTENSION));
    Assert.assertTrue(rawCoverage.records().stream().noneMatch(t -> t.getContig().equals("2") || t.getContig().equals("3")));
    final File targetsFile = new File(outputFile.getAbsolutePath() + ".targets.tsv");
    final List<Target> targets = TargetTableReader.readTargetFile(targetsFile);
    Assert.assertTrue(targets.stream().allMatch(t -> t.getContig().equals("1")));
}

Example 63 with Target

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

the class GermlinePloidyAnnotatedTargetCollectionUnitTest method testNonUniqueTargetNames.

/* check if targets have unique names */
@Test(expectedExceptions = IllegalArgumentException.class)
public void testNonUniqueTargetNames() {
    final List<Target> badTargetList = Arrays.stream(new Target[] { new Target("NON_UNIQUE_NAME", new SimpleInterval("1", 1, 10)), new Target("NON_UNIQUE_NAME", new SimpleInterval("1", 10, 20)) }).collect(Collectors.toList());
    new GermlinePloidyAnnotatedTargetCollection(contigPloidyAnnotsList, badTargetList);
}

Example 64 with Target

use of org.broadinstitute.hellbender.tools.exome.Target in project gatk-protected 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 65 with Target

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

the class XHMMSegmentGenotyperIntegrationTest method assertVariantSegmentsAreCovered.

private void assertVariantSegmentsAreCovered(final List<VariantContext> variants, final List<HiddenStateSegmentRecord<CopyNumberTriState, Target>> variantSegments) {
    for (final HiddenStateSegmentRecord<CopyNumberTriState, Target> variantSegment : variantSegments) {
        final Optional<VariantContext> match = variants.stream().filter(vc -> new SimpleInterval(vc).equals(variantSegment.getSegment().getInterval())).findFirst();
        Assert.assertTrue(match.isPresent());
        final VariantContext matchedVariant = match.get();
        final Genotype genotype = matchedVariant.getGenotype(variantSegment.getSampleName());
        final String discovery = genotype.getAnyAttribute(XHMMSegmentGenotyper.DISCOVERY_KEY).toString();
        Assert.assertTrue(discovery.equals(XHMMSegmentGenotyper.DISCOVERY_TRUE));
        final CopyNumberTriState call = variantSegment.getSegment().getCall();
        final List<Allele> gt = genotype.getAlleles();
        Assert.assertEquals(gt.size(), 1);
        // The call may not be the same for case where the event-quality is relatively low.
        if (variantSegment.getSegment().getEventQuality() > 10) {
            Assert.assertEquals(CopyNumberTriStateAllele.valueOf(gt.get(0)).state, call, genotype.toString());
        }
        final String[] SQ = genotype.getAnyAttribute(XHMMSegmentGenotyper.SOME_QUALITY_KEY).toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR);
        final double someQual = variantSegment.getSegment().getSomeQuality();
        Assert.assertEquals(Double.parseDouble(SQ[call == CopyNumberTriState.DELETION ? 0 : 1]), someQual, XHMMSegmentGenotyper.PHRED_SCORE_PRECISION, variantSegment.getSampleName() + " => " + genotype.toString());
        final String[] LQ = genotype.getAnyAttribute(XHMMSegmentGenotyper.START_QUALITY_KEY).toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR);
        final double startQuality = variantSegment.getSegment().getStartQuality();
        Assert.assertEquals(Double.parseDouble(LQ[call == CopyNumberTriState.DELETION ? 0 : 1]), startQuality, XHMMSegmentGenotyper.PHRED_SCORE_PRECISION, variantSegment.getSampleName() + " => " + genotype.toString());
        final String[] RQ = genotype.getAnyAttribute(XHMMSegmentGenotyper.END_QUALITY_KEY).toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR);
        final double endQuality = variantSegment.getSegment().getEndQuality();
        Assert.assertEquals(Double.parseDouble(RQ[call == CopyNumberTriState.DELETION ? 0 : 1]), endQuality, XHMMSegmentGenotyper.PHRED_SCORE_PRECISION, variantSegment.getSampleName() + " => " + genotype.toString());
        // Check the PL.
        final int[] PL = genotype.getPL();
        final int observedGQFromPL = Math.min(XHMMSegmentGenotyper.MAX_GQ, PL[CopyNumberTriStateAllele.REF.index()] - PL[CopyNumberTriStateAllele.valueOf(call).index()]);
        final double expectedCallPL = GATKProtectedMathUtils.roundPhred(QualityUtils.phredScaleErrorRate(QualityUtils.qualToProb(variantSegment.getSegment().getExactQuality())), HMMPostProcessor.PHRED_SCORE_PRECISION);
        final double expectedRefPL = GATKProtectedMathUtils.roundPhred(QualityUtils.phredScaleCorrectRate(QualityUtils.qualToProb(variantSegment.getSegment().getEventQuality())), HMMPostProcessor.PHRED_SCORE_PRECISION);
        final int expectedGQFromPL = Math.min(XHMMSegmentGenotyper.MAX_GQ, (int) Math.round(expectedRefPL - expectedCallPL));
        Assert.assertTrue(Math.abs(observedGQFromPL - expectedGQFromPL) <= 1, genotype.toString() + " " + variantSegment.getSegment().getEventQuality());
    }
}