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

Example 6 with ModeledSegment

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

the class PerformAlleleFractionSegmentation method doWork.

@Override
public Object doWork() {
    final String sampleName = FilenameUtils.getBaseName(snpCountsFile.getAbsolutePath());
    final AllelicPanelOfNormals allelicPoN = allelicPoNFile != null ? AllelicPanelOfNormals.read(allelicPoNFile) : AllelicPanelOfNormals.EMPTY_PON;
    final AllelicCountCollection acc = new AllelicCountCollection(snpCountsFile);
    final AlleleFractionSegmenter segmenter = new AlleleFractionSegmenter(initialNumStates, acc, allelicPoN);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    SegmentUtils.writeModeledSegmentFile(outputSegmentsFile, segments, sampleName, true);
    return "SUCCESS";
}

Example 7 with ModeledSegment

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

the class CopyRatioSegmenterUnitTest method testSegmentation.

@Test
public void testSegmentation() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final List<Double> trueWeights = Arrays.asList(0.2, 0.5, 0.3);
    final List<Double> trueLog2CopyRatios = Arrays.asList(-2.0, 0.0, 1.4);
    final double trueMemoryLength = 1e5;
    final double trueStandardDeviation = 0.2;
    final CopyRatioHMM trueModel = new CopyRatioHMM(trueLog2CopyRatios, trueWeights, trueMemoryLength, trueStandardDeviation);
    final int chainLength = 10000;
    final List<SimpleInterval> positions = randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    final List<Integer> trueStates = trueModel.generateHiddenStateChain(positions);
    final List<Double> trueLog2CopyRatioSequence = trueStates.stream().map(n -> trueLog2CopyRatios.get(n)).collect(Collectors.toList());
    final List<Double> data = trueLog2CopyRatioSequence.stream().map(cr -> generateData(trueStandardDeviation, cr, rng)).collect(Collectors.toList());
    final List<Target> targets = positions.stream().map(Target::new).collect(Collectors.toList());
    final ReadCountCollection rcc = new ReadCountCollection(targets, Arrays.asList("SAMPLE"), new Array2DRowRealMatrix(data.stream().mapToDouble(x -> x).toArray()));
    final CopyRatioSegmenter segmenter = new CopyRatioSegmenter(10, rcc);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    final double[] segmentCopyRatios = segments.stream().flatMap(s -> Collections.nCopies((int) s.getTargetCount(), s.getSegmentMeanInLog2CRSpace()).stream()).mapToDouble(x -> x).toArray();
    final double averageCopyRatioError = IntStream.range(0, trueLog2CopyRatioSequence.size()).mapToDouble(n -> Math.abs(segmentCopyRatios[n] - trueLog2CopyRatioSequence.get(n))).average().getAsDouble();
    Assert.assertEquals(averageCopyRatioError, 0, 0.025);
}

Example 8 with ModeledSegment

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

the class PerformAlleleFractionSegmentationIntegrationTest method testCommandLine.

// checks that segmentation output is created -- only the unit test checks correctness of results
@Test
public void testCommandLine() {
    final File snpFile = ALLELIC_COUNTS_FILE;
    final File outputSegmentFile = createTempFile("segments", ".seg");
    final int initialNumStates = 10;
    final String[] arguments = { "-" + ExomeStandardArgumentDefinitions.TUMOR_ALLELIC_COUNTS_FILE_SHORT_NAME, snpFile.getAbsolutePath(), "-" + PerformAlleleFractionSegmentation.INITIAL_NUM_STATES_SHORT_NAME, Integer.toString(initialNumStates), "-" + ExomeStandardArgumentDefinitions.SEGMENT_FILE_SHORT_NAME, outputSegmentFile.getAbsolutePath() };
    runCommandLine(arguments);
    final List<ModeledSegment> segments = SegmentUtils.readModeledSegmentsFromSegmentFile(outputSegmentFile);
}

Example 9 with ModeledSegment

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

the class PerformCopyRatioSegmentationIntegrationTest method testCommandLine.

// checks that segmentation output is created -- only the unit test checks correctness of results
@Test
public void testCommandLine() throws IOException {
    final File tnCoverageFile = LOG2_TN_COVERAGE_FILE;
    final File outputSegmentFile = createTempFile("segments", ".seg");
    final int initialNumStates = 10;
    final String[] arguments = { "-" + ExomeStandardArgumentDefinitions.TANGENT_NORMALIZED_COUNTS_FILE_SHORT_NAME, tnCoverageFile.getAbsolutePath(), "-" + PerformCopyRatioSegmentation.INITIAL_NUM_STATES_SHORT_NAME, Integer.toString(initialNumStates), "-" + ExomeStandardArgumentDefinitions.SEGMENT_FILE_SHORT_NAME, outputSegmentFile.getAbsolutePath() };
    runCommandLine(arguments);
    final List<ModeledSegment> segments = SegmentUtils.readModeledSegmentsFromSegmentFile(outputSegmentFile);
}

Example 10 with ModeledSegment

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

the class AlleleFractionSegmenterUnitTest method testChromosomesOnDifferentSegments.

@Test
public void testChromosomesOnDifferentSegments() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final double[] trueMinorAlleleFractions = new double[] { 0.12, 0.32, 0.5 };
    final double trueMemoryLength = 1e5;
    final AlleleFractionGlobalParameters trueParams = new AlleleFractionGlobalParameters(1.0, 0.01, 0.01);
    // randomly set positions
    final int chainLength = 100;
    final List<SimpleInterval> positions = CopyRatioSegmenterUnitTest.randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    positions.addAll(CopyRatioSegmenterUnitTest.randomPositions("chr2", chainLength, rng, trueMemoryLength / 4));
    positions.addAll(CopyRatioSegmenterUnitTest.randomPositions("chr3", chainLength, rng, trueMemoryLength / 4));
    //fix everything to the same state 2
    final int trueState = 2;
    final List<Double> minorAlleleFractionSequence = Collections.nCopies(positions.size(), trueMinorAlleleFractions[trueState]);
    final AllelicCountCollection counts = generateCounts(minorAlleleFractionSequence, positions, rng, trueParams);
    final AlleleFractionSegmenter segmenter = new AlleleFractionSegmenter(10, counts, AllelicPanelOfNormals.EMPTY_PON);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    //check that each chromosome has at least one segment
    final int numDifferentContigsInSegments = (int) segments.stream().map(ModeledSegment::getContig).distinct().count();
    Assert.assertEquals(numDifferentContigsInSegments, 3);
}