Examples with BiFunction java.util.function.BiFunction used on opensource projects

Example 41 with BiFunction

use of java.util.function.BiFunction 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 42 with BiFunction

use of java.util.function.BiFunction in project gatk-protected by broadinstitute.

the class ReadCountRecordUnitTest method testAppendCountsTo.

@Test(dataProvider = "testData", dependsOnMethods = "testCreation")
public void testAppendCountsTo(@SuppressWarnings("unused") final String testName, final BiFunction<Target, double[], ? extends ReadCountRecord> constructor, final int size) {
    final double[] counts = generateCounts(size);
    final boolean round = testName.equals("long[]");
    final ReadCountRecord record = constructor.apply(TEST_TARGET, counts);
    final List<String> columnNames = Stream.concat(Stream.concat(IntStream.range(0, 10).mapToObj(i -> "pre-padding_" + i), IntStream.range(0, counts.length).mapToObj(i -> "column_" + i)), IntStream.range(0, 10).mapToObj(i -> "post-padding_" + i)).collect(Collectors.toList());
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final DataLine dataLine = new DataLine(columns, RuntimeException::new);
    final double[] copiedCounts = new double[counts.length + 20];
    Arrays.fill(copiedCounts, -11);
    for (int i = 0; i < 10 + 10 + counts.length; i++) {
        dataLine.append("-11");
    }
    dataLine.seek(10);
    record.appendCountsTo(dataLine);
    // Check the copied values.
    if (!round) {
        for (int i = 0; i < counts.length; i++) {
            Assert.assertEquals(dataLine.getDouble(10 + i), counts[i], 0.0);
        }
    } else {
        for (int i = 0; i < counts.length; i++) {
            Assert.assertEquals(dataLine.getDouble(10 + i), Math.round(counts[i]), 0.00001);
        }
    }
    // Check that the padding remains intact:
    for (int i = 0; i < 10; i++) {
        Assert.assertEquals(dataLine.get(i), "-11");
    }
    for (int i = counts.length + 10; i < copiedCounts.length; i++) {
        Assert.assertEquals(dataLine.get(i), "-11");
    }
}

Example 43 with BiFunction

use of java.util.function.BiFunction in project gatk-protected by broadinstitute.

the class ReadCountRecordUnitTest method testAppendCountsToBeyondEnd.

@Test(dataProvider = "testNonZeroCountsData", dependsOnMethods = "testAppendCountsTo", expectedExceptions = IllegalStateException.class)
public void testAppendCountsToBeyondEnd(@SuppressWarnings("unused") final String testName, final BiFunction<Target, double[], ? extends ReadCountRecord> constructor, final int size) {
    final double[] counts = generateCounts(size);
    final ReadCountRecord record = constructor.apply(TEST_TARGET, counts);
    final List<String> columnNames = Stream.concat(Stream.concat(IntStream.range(0, 10).mapToObj(i -> "pre-padding_" + i), IntStream.range(0, counts.length).mapToObj(i -> "column_" + i)), IntStream.range(0, 10).mapToObj(i -> "post-padding_" + i)).collect(Collectors.toList());
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final DataLine dataLine = new DataLine(columns, RuntimeException::new);
    final double[] copiedCounts = new double[counts.length + 20];
    Arrays.fill(copiedCounts, -11);
    dataLine.seek(columnNames.size());
    record.appendCountsTo(dataLine);
}