Examples with Tuple2 scala.Tuple2 used on opensource projects

Example 76 with Tuple2

use of scala.Tuple2 in project gatk by broadinstitute.

the class ReadsForQNamesFinder method call.

public Iterable<Tuple2<Integer, List<SVFastqUtils.FastqRead>>> call(final Iterator<GATKRead> readsItr) {
    @SuppressWarnings({ "unchecked", "rawtypes" }) final List<SVFastqUtils.FastqRead>[] intervalReads = new List[nIntervals];
    int nPopulatedIntervals = 0;
    while (readsItr.hasNext()) {
        final GATKRead read = readsItr.next();
        final Iterator<QNameAndInterval> namesItr = qNamesMultiMap.findEach(read.getName());
        SVFastqUtils.FastqRead FastqRead = null;
        while (namesItr.hasNext()) {
            final int intervalId = namesItr.next().getIntervalId();
            if (intervalReads[intervalId] == null) {
                intervalReads[intervalId] = new ArrayList<>(nReadsPerInterval);
                nPopulatedIntervals += 1;
            }
            if (FastqRead == null) {
                final String readName = dumpFASTQs ? SVFastqUtils.readToFastqSeqId(read, includeMappingLocation) : null;
                FastqRead = new SVFastqUtils.FastqRead(readName, read.getBases(), read.getBaseQualities());
            }
            intervalReads[intervalId].add(FastqRead);
        }
    }
    final List<Tuple2<Integer, List<SVFastqUtils.FastqRead>>> fastQRecords = new ArrayList<>(nPopulatedIntervals);
    if (nPopulatedIntervals > 0) {
        for (int idx = 0; idx != nIntervals; ++idx) {
            final List<SVFastqUtils.FastqRead> readList = intervalReads[idx];
            if (readList != null)
                fastQRecords.add(new Tuple2<>(idx, readList));
        }
    }
    return fastQRecords;
}

Example 77 with Tuple2

use of scala.Tuple2 in project gatk by broadinstitute.

the class RunSGAViaProcessBuilderOnSpark method writeToLocal.

/**
     * Utility function that unloads the FASTQ contents for a breakpoint to a local file for later consumption by SGA.
     * @param oneBreakPoint input for one breakpoint, where the first is the path to the FASTQ file and the second is the FASTQ file's content
     * @return              the breakpoint ID and with the FASTQ file contents dumped to a local File
     * @throws IOException  if fails to create the temporary directory or fails to write to local file
     */
@VisibleForTesting
static Tuple2<Long, File> writeToLocal(final Tuple2<String, String> oneBreakPoint, final String subStringToStripout) throws IOException {
    final String fastqFilename = FilenameUtils.getName(oneBreakPoint._1());
    final File localTempWorkingDir = Files.createTempDirectory(fastqFilename + "_").toAbsolutePath().toFile();
    localTempWorkingDir.deleteOnExit();
    final File localFASTQFile = new File(localTempWorkingDir, fastqFilename);
    FileUtils.writeStringToFile(localFASTQFile, oneBreakPoint._2());
    final Long breakpointID = Long.parseLong(FilenameUtils.getBaseName(oneBreakPoint._1()).replace(subStringToStripout, ""));
    return new Tuple2<>(breakpointID, localFASTQFile);
}

Example 78 with Tuple2

use of scala.Tuple2 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 79 with Tuple2

use of scala.Tuple2 in project gatk by broadinstitute.

the class ShuffleJoinReadsWithRefBases method addBases.

/**
     * Joins each read of an RDD<GATKRead, T> with key's corresponding reference sequence.
     *
     * @param referenceDataflowSource The source of the reference sequence information
     * @param keyedByRead The read-keyed RDD for which to extract reference sequence information
     * @return The JavaPairRDD that contains each read along with the corresponding ReferenceBases object and the value
     */
public static <T> JavaPairRDD<GATKRead, Tuple2<T, ReferenceBases>> addBases(final ReferenceMultiSource referenceDataflowSource, final JavaPairRDD<GATKRead, T> keyedByRead) {
    SerializableFunction<GATKRead, SimpleInterval> windowFunction = referenceDataflowSource.getReferenceWindowFunction();
    JavaPairRDD<ReferenceShard, Tuple2<GATKRead, T>> shardRead = keyedByRead.mapToPair(pair -> {
        ReferenceShard shard = ReferenceShard.getShardNumberFromInterval(windowFunction.apply(pair._1()));
        return new Tuple2<>(shard, pair);
    });
    JavaPairRDD<ReferenceShard, Iterable<Tuple2<GATKRead, T>>> shardiRead = shardRead.groupByKey();
    return shardiRead.flatMapToPair(in -> {
        List<Tuple2<GATKRead, Tuple2<T, ReferenceBases>>> out = Lists.newArrayList();
        Iterable<Tuple2<GATKRead, T>> iReads = in._2();
        final List<SimpleInterval> readWindows = Utils.stream(iReads).map(pair -> windowFunction.apply(pair._1())).collect(Collectors.toList());
        SimpleInterval interval = IntervalUtils.getSpanningInterval(readWindows);
        ReferenceBases bases = referenceDataflowSource.getReferenceBases(null, interval);
        for (Tuple2<GATKRead, T> p : iReads) {
            final ReferenceBases subset = bases.getSubset(windowFunction.apply(p._1()));
            out.add(new Tuple2<>(p._1(), new Tuple2<>(p._2(), subset)));
        }
        return out.iterator();
    });
}

Example 80 with Tuple2

use of scala.Tuple2 in project gatk by broadinstitute.

the class ShuffleJoinReadsWithVariants method pairReadsWithVariantShards.

private static JavaPairRDD<VariantShard, GATKRead> pairReadsWithVariantShards(final JavaRDD<GATKRead> reads) {
    return reads.flatMapToPair(gatkRead -> {
        List<VariantShard> shards = VariantShard.getVariantShardsFromInterval(gatkRead);
        List<Tuple2<VariantShard, GATKRead>> out = Lists.newArrayList();
        for (VariantShard shard : shards) {
            out.add(new Tuple2<>(shard, gatkRead));
        }
        return out.iterator();
    });
}