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

Example 6 with ACNVModeledSegment

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

the class AllelicSplitCallerModelStateUnitTest method testSerializationRoundTrip.

@Test
public void testSerializationRoundTrip() {
    final ACNVModeledSegment acnvModeledSegment = new ACNVModeledSegment(new SimpleInterval("1", 1000, 1500), new PosteriorSummary(-4000, -4001, -4002), new PosteriorSummary(-4000, -4001, -4002));
    final List<ACNVModeledSegment> tempList = new ArrayList<>();
    tempList.add(acnvModeledSegment);
    final AllelicBalanceCallerModelState state = AllelicBalanceCallerModelState.createInitialCNLOHCallerModelState(0.2, tempList, HomoSapiensConstants.DEFAULT_PLOIDY, CNLOHCaller.NUM_RHOS);
    SparkTestUtils.roundTripInKryo(state, AllelicBalanceCallerModelState.class, SparkContextFactory.getTestSparkContext().getConf());
}

Example 7 with ACNVModeledSegment

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

the class AllelicSplitCallerUnitTest method testMakeCalls.

@Test
public void testMakeCalls() {
    // This mostly just checks that the calling does not crash and does produce results.
    final CNLOHCaller cnlohCaller = new CNLOHCaller();
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final List<ACNVModeledSegment> segs = SegmentUtils.readACNVModeledSegmentFile(ACNV_SEG_FILE);
    SparkTestUtils.roundTripInKryo(segs.get(0), ACNVModeledSegment.class, ctx.getConf());
    // Make sure the CNLOH Caller is serializable before making calls.
    SparkTestUtils.roundTripInKryo(cnlohCaller, CNLOHCaller.class, ctx.getConf());
    final List<AllelicCalls> calls = cnlohCaller.makeCalls(segs, 2, ctx);
    Assert.assertNotNull(calls);
    Assert.assertTrue(calls.size() > 0);
    Assert.assertTrue(calls.stream().allMatch(c -> c.getBalancedCall() != null));
    Assert.assertTrue(calls.stream().allMatch(c -> c.getCnlohCall() != null));
    Assert.assertTrue(calls.stream().allMatch(c -> c.getAcnvSegment() != null));
    // Make sure the CNLOH Caller is serializable after making calls.
    SparkTestUtils.roundTripInKryo(cnlohCaller, CNLOHCaller.class, ctx.getConf());
    SparkTestUtils.roundTripInKryo(calls.get(0), AllelicCalls.class, ctx.getConf());
}

Example 8 with ACNVModeledSegment

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

the class AllelicSplitCallerModelStateUnitTest method testBasicInit.

@Test
public void testBasicInit() {
    final ACNVModeledSegment acnvModeledSegment = new ACNVModeledSegment(new SimpleInterval("1", 1000, 1500), new PosteriorSummary(-4000, -4001, -4002), new PosteriorSummary(-4000, -4001, -4002));
    final List<ACNVModeledSegment> tempList = new ArrayList<>();
    tempList.add(acnvModeledSegment);
    final AllelicBalanceCallerModelState state = AllelicBalanceCallerModelState.createInitialCNLOHCallerModelState(0.2, tempList, HomoSapiensConstants.DEFAULT_PLOIDY, CNLOHCaller.NUM_RHOS);
    Assert.assertNotNull(state);
    Assert.assertNotNull(state.getEffectivePis());
    Assert.assertTrue(state.getEffectivePis().length > 0);
    Assert.assertTrue(state.getmVals().length > 0);
    Assert.assertTrue(state.getnVals().length > 0);
    Assert.assertEquals(MathUtils.sum(state.getEffectivePis()), 1.0, 1e-10);
}

Example 9 with ACNVModeledSegment

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

the class AllelicSplitCallerUnitTest method testMakeCalls.

@Test
public void testMakeCalls() {
    // This mostly just checks that the calling does not crash and does produce results.
    final CNLOHCaller cnlohCaller = new CNLOHCaller();
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final List<ACNVModeledSegment> segs = SegmentUtils.readACNVModeledSegmentFile(ACNV_SEG_FILE);
    SparkTestUtils.roundTripInKryo(segs.get(0), ACNVModeledSegment.class, ctx.getConf());
    // Make sure the CNLOH Caller is serializable before making calls.
    SparkTestUtils.roundTripInKryo(cnlohCaller, CNLOHCaller.class, ctx.getConf());
    final List<AllelicCalls> calls = cnlohCaller.makeCalls(segs, 2, ctx);
    Assert.assertNotNull(calls);
    Assert.assertTrue(calls.size() > 0);
    Assert.assertTrue(calls.stream().allMatch(c -> c.getBalancedCall() != null));
    Assert.assertTrue(calls.stream().allMatch(c -> c.getCnlohCall() != null));
    Assert.assertTrue(calls.stream().allMatch(c -> c.getAcnvSegment() != null));
    // Make sure the CNLOH Caller is serializable after making calls.
    SparkTestUtils.roundTripInKryo(cnlohCaller, CNLOHCaller.class, ctx.getConf());
    SparkTestUtils.roundTripInKryo(calls.get(0), AllelicCalls.class, ctx.getConf());
}

Example 10 with ACNVModeledSegment

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

the class CNLOHCaller method calcNewRhos.

private double[] calcNewRhos(final List<ACNVModeledSegment> segments, final List<double[][][]> responsibilitiesBySeg, final double lambda, final double[] rhos, final int[] mVals, final int[] nVals, final JavaSparkContext ctx) {
    // Since, we pass in the entire responsibilities matrix, we need the correct index for each rho.  That, and the
    //  fact that this is a univariate objective function, means we need to create an instance for each rho.  And
    //  then we blast across Spark.
    final List<Pair<? extends Function<Double, Double>, SearchInterval>> objectives = IntStream.range(0, rhos.length).mapToObj(i -> new Pair<>(new Function<Double, Double>() {

        @Override
        public Double apply(Double rho) {
            return calculateESmnObjective(rho, segments, responsibilitiesBySeg, mVals, nVals, lambda, i);
        }
    }, new SearchInterval(0.0, 1.0, rhos[i]))).collect(Collectors.toList());
    final JavaRDD<Pair<? extends Function<Double, Double>, SearchInterval>> objectivesRDD = ctx.parallelize(objectives);
    final List<Double> resultsAsDouble = objectivesRDD.map(objective -> optimizeIt(objective.getFirst(), objective.getSecond())).collect();
    return resultsAsDouble.stream().mapToDouble(Double::doubleValue).toArray();
}