Examples with HMMSegmentProcessor org.broadinstitute.hellbender.utils.hmm.segmentation.HMMSegmentProcessor used on opensource projects

Example 1 with HMMSegmentProcessor

use of org.broadinstitute.hellbender.utils.hmm.segmentation.HMMSegmentProcessor in project gatk by broadinstitute.

the class CoverageModelEMWorkspace method getCopyRatioSegmentsSpark.

/**
     * Fetch copy ratio segments from compute blocks (Spark implementation)
     *
     * @return a list of {@link CopyRatioHMMResults}
     */
private List<List<HiddenStateSegmentRecord<STATE, Target>>> getCopyRatioSegmentsSpark() {
    /* local final member variables for lambda capture */
    final List<Target> processedTargetList = new ArrayList<>();
    processedTargetList.addAll(this.processedTargetList);
    final List<SexGenotypeData> processedSampleSexGenotypeData = new ArrayList<>();
    processedSampleSexGenotypeData.addAll(this.processedSampleSexGenotypeData);
    final List<String> processedSampleNameList = new ArrayList<>();
    processedSampleNameList.addAll(this.processedSampleNameList);
    final INDArray sampleReadDepths = Transforms.exp(sampleMeanLogReadDepths, true);
    final CopyRatioExpectationsCalculator<CoverageModelCopyRatioEmissionData, STATE> copyRatioExpectationsCalculator = this.copyRatioExpectationsCalculator;
    final BiFunction<SexGenotypeData, Target, STATE> referenceStateFactory = this.referenceStateFactory;
    return fetchCopyRatioEmissionDataSpark().mapPartitionsToPair(it -> {
        final List<Tuple2<Integer, CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE>>> newPartitionData = new ArrayList<>();
        while (it.hasNext()) {
            final Tuple2<Integer, List<CoverageModelCopyRatioEmissionData>> prevDatum = it.next();
            final int sampleIndex = prevDatum._1;
            final CopyRatioCallingMetadata copyRatioCallingMetadata = CopyRatioCallingMetadata.builder().sampleName(processedSampleNameList.get(sampleIndex)).sampleSexGenotypeData(processedSampleSexGenotypeData.get(sampleIndex)).sampleCoverageDepth(sampleReadDepths.getDouble(sampleIndex)).emissionCalculationStrategy(EmissionCalculationStrategy.HYBRID_POISSON_GAUSSIAN).build();
            newPartitionData.add(new Tuple2<>(sampleIndex, copyRatioExpectationsCalculator.getCopyRatioHMMResults(copyRatioCallingMetadata, processedTargetList, prevDatum._2)));
        }
        return newPartitionData.iterator();
    }, true).mapPartitionsToPair(it -> {
        final List<Tuple2<Integer, List<HiddenStateSegmentRecord<STATE, Target>>>> newPartitionData = new ArrayList<>();
        while (it.hasNext()) {
            final Tuple2<Integer, CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE>> prevDatum = it.next();
            final int sampleIndex = prevDatum._1;
            final CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE> result = prevDatum._2;
            final HMMSegmentProcessor<CoverageModelCopyRatioEmissionData, STATE, Target> processor = new HMMSegmentProcessor<>(Collections.singletonList(result.getMetaData().getSampleName()), Collections.singletonList(result.getMetaData().getSampleSexGenotypeData()), referenceStateFactory, Collections.singletonList(new HashedListTargetCollection<>(processedTargetList)), Collections.singletonList(result.getForwardBackwardResult()), Collections.singletonList(result.getViterbiResult()));
            newPartitionData.add(new Tuple2<>(sampleIndex, processor.getSegmentsAsList()));
        }
        return newPartitionData.iterator();
    }).collect().stream().sorted(Comparator.comparingInt(t -> t._1)).map(t -> t._2).collect(Collectors.toList());
}

Example 2 with HMMSegmentProcessor

use of org.broadinstitute.hellbender.utils.hmm.segmentation.HMMSegmentProcessor in project gatk by broadinstitute.

the class CoverageModelEMWorkspace method getCopyRatioSegmentsLocal.

private List<List<HiddenStateSegmentRecord<STATE, Target>>> getCopyRatioSegmentsLocal() {
    final List<List<CoverageModelCopyRatioEmissionData>> copyRatioEmissionData = fetchCopyRatioEmissionDataLocal();
    final INDArray sampleReadDepths = Transforms.exp(sampleMeanLogReadDepths, true);
    return sampleIndexStream().mapToObj(si -> {
        final CopyRatioCallingMetadata metadata = CopyRatioCallingMetadata.builder().sampleName(processedSampleNameList.get(si)).sampleSexGenotypeData(processedSampleSexGenotypeData.get(si)).sampleCoverageDepth(sampleReadDepths.getDouble(si)).emissionCalculationStrategy(EmissionCalculationStrategy.HYBRID_POISSON_GAUSSIAN).build();
        return copyRatioExpectationsCalculator.getCopyRatioHMMResults(metadata, processedTargetList, copyRatioEmissionData.get(si));
    }).map(result -> {
        final HMMSegmentProcessor<CoverageModelCopyRatioEmissionData, STATE, Target> processor = new HMMSegmentProcessor<>(Collections.singletonList(result.getMetaData().getSampleName()), Collections.singletonList(result.getMetaData().getSampleSexGenotypeData()), referenceStateFactory, Collections.singletonList(new HashedListTargetCollection<>(processedTargetList)), Collections.singletonList(result.getForwardBackwardResult()), Collections.singletonList(result.getViterbiResult()));
        return processor.getSegmentsAsList();
    }).collect(Collectors.toList());
}

Example 3 with HMMSegmentProcessor

use of org.broadinstitute.hellbender.utils.hmm.segmentation.HMMSegmentProcessor in project gatk-protected by broadinstitute.

the class CoverageModelEMWorkspace method getCopyRatioSegmentsSpark.

/**
     * Fetch copy ratio segments from compute blocks (Spark implementation)
     *
     * @return a list of {@link CopyRatioHMMResults}
     */
private List<List<HiddenStateSegmentRecord<STATE, Target>>> getCopyRatioSegmentsSpark() {
    /* local final member variables for lambda capture */
    final List<Target> processedTargetList = new ArrayList<>();
    processedTargetList.addAll(this.processedTargetList);
    final List<SexGenotypeData> processedSampleSexGenotypeData = new ArrayList<>();
    processedSampleSexGenotypeData.addAll(this.processedSampleSexGenotypeData);
    final List<String> processedSampleNameList = new ArrayList<>();
    processedSampleNameList.addAll(this.processedSampleNameList);
    final INDArray sampleReadDepths = Transforms.exp(sampleMeanLogReadDepths, true);
    final CopyRatioExpectationsCalculator<CoverageModelCopyRatioEmissionData, STATE> copyRatioExpectationsCalculator = this.copyRatioExpectationsCalculator;
    final BiFunction<SexGenotypeData, Target, STATE> referenceStateFactory = this.referenceStateFactory;
    return fetchCopyRatioEmissionDataSpark().mapPartitionsToPair(it -> {
        final List<Tuple2<Integer, CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE>>> newPartitionData = new ArrayList<>();
        while (it.hasNext()) {
            final Tuple2<Integer, List<CoverageModelCopyRatioEmissionData>> prevDatum = it.next();
            final int sampleIndex = prevDatum._1;
            final CopyRatioCallingMetadata copyRatioCallingMetadata = CopyRatioCallingMetadata.builder().sampleName(processedSampleNameList.get(sampleIndex)).sampleSexGenotypeData(processedSampleSexGenotypeData.get(sampleIndex)).sampleCoverageDepth(sampleReadDepths.getDouble(sampleIndex)).emissionCalculationStrategy(EmissionCalculationStrategy.HYBRID_POISSON_GAUSSIAN).build();
            newPartitionData.add(new Tuple2<>(sampleIndex, copyRatioExpectationsCalculator.getCopyRatioHMMResults(copyRatioCallingMetadata, processedTargetList, prevDatum._2)));
        }
        return newPartitionData.iterator();
    }, true).mapPartitionsToPair(it -> {
        final List<Tuple2<Integer, List<HiddenStateSegmentRecord<STATE, Target>>>> newPartitionData = new ArrayList<>();
        while (it.hasNext()) {
            final Tuple2<Integer, CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE>> prevDatum = it.next();
            final int sampleIndex = prevDatum._1;
            final CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE> result = prevDatum._2;
            final HMMSegmentProcessor<CoverageModelCopyRatioEmissionData, STATE, Target> processor = new HMMSegmentProcessor<>(Collections.singletonList(result.getMetaData().getSampleName()), Collections.singletonList(result.getMetaData().getSampleSexGenotypeData()), referenceStateFactory, Collections.singletonList(new HashedListTargetCollection<>(processedTargetList)), Collections.singletonList(result.getForwardBackwardResult()), Collections.singletonList(result.getViterbiResult()));
            newPartitionData.add(new Tuple2<>(sampleIndex, processor.getSegmentsAsList()));
        }
        return newPartitionData.iterator();
    }).collect().stream().sorted(Comparator.comparingInt(t -> t._1)).map(t -> t._2).collect(Collectors.toList());
}

Example 4 with HMMSegmentProcessor

use of org.broadinstitute.hellbender.utils.hmm.segmentation.HMMSegmentProcessor in project gatk-protected by broadinstitute.

the class CoverageModelEMWorkspace method getCopyRatioSegmentsLocal.

private List<List<HiddenStateSegmentRecord<STATE, Target>>> getCopyRatioSegmentsLocal() {
    final List<List<CoverageModelCopyRatioEmissionData>> copyRatioEmissionData = fetchCopyRatioEmissionDataLocal();
    final INDArray sampleReadDepths = Transforms.exp(sampleMeanLogReadDepths, true);
    return sampleIndexStream().mapToObj(si -> {
        final CopyRatioCallingMetadata metadata = CopyRatioCallingMetadata.builder().sampleName(processedSampleNameList.get(si)).sampleSexGenotypeData(processedSampleSexGenotypeData.get(si)).sampleCoverageDepth(sampleReadDepths.getDouble(si)).emissionCalculationStrategy(EmissionCalculationStrategy.HYBRID_POISSON_GAUSSIAN).build();
        return copyRatioExpectationsCalculator.getCopyRatioHMMResults(metadata, processedTargetList, copyRatioEmissionData.get(si));
    }).map(result -> {
        final HMMSegmentProcessor<CoverageModelCopyRatioEmissionData, STATE, Target> processor = new HMMSegmentProcessor<>(Collections.singletonList(result.getMetaData().getSampleName()), Collections.singletonList(result.getMetaData().getSampleSexGenotypeData()), referenceStateFactory, Collections.singletonList(new HashedListTargetCollection<>(processedTargetList)), Collections.singletonList(result.getForwardBackwardResult()), Collections.singletonList(result.getViterbiResult()));
        return processor.getSegmentsAsList();
    }).collect(Collectors.toList());
}