Examples with HopscotchUniqueMultiMap org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMap used on opensource projects

Example 1 with HopscotchUniqueMultiMap

use of org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMap in project gatk by broadinstitute.

the class FindBreakpointEvidenceSpark method getKmerIntervals.

/** find kmers for each interval */
@VisibleForTesting
static Tuple2<List<AlignedAssemblyOrExcuse>, List<KmerAndInterval>> getKmerIntervals(final Params params, final JavaSparkContext ctx, final HopscotchUniqueMultiMap<String, Integer, QNameAndInterval> qNamesMultiMap, final int nIntervals, final Set<SVKmer> kmerKillSet, final JavaRDD<GATKRead> reads, final Locations locations) {
    final Broadcast<Set<SVKmer>> broadcastKmerKillSet = ctx.broadcast(kmerKillSet);
    final Broadcast<HopscotchUniqueMultiMap<String, Integer, QNameAndInterval>> broadcastQNameAndIntervalsMultiMap = ctx.broadcast(qNamesMultiMap);
    // given a set of template names with interval IDs and a kill set of ubiquitous kmers,
    // produce a set of interesting kmers for each interval ID
    final int kmersPerPartitionGuess = params.cleanerKmersPerPartitionGuess;
    final int minKmers = params.cleanerMinKmerCount;
    final int maxKmers = params.cleanerMaxKmerCount;
    final int maxIntervals = params.cleanerMaxIntervals;
    final int kSize = params.kSize;
    final int maxDUSTScore = params.maxDUSTScore;
    final List<KmerAndInterval> kmerIntervals = reads.mapPartitionsToPair(readItr -> new MapPartitioner<>(readItr, new QNameKmerizer(broadcastQNameAndIntervalsMultiMap.value(), broadcastKmerKillSet.value(), kSize, maxDUSTScore)).iterator(), false).reduceByKey(Integer::sum).mapPartitions(itr -> new KmerCleaner(itr, kmersPerPartitionGuess, minKmers, maxKmers, maxIntervals).iterator()).collect();
    broadcastQNameAndIntervalsMultiMap.destroy();
    broadcastKmerKillSet.destroy();
    final int[] intervalKmerCounts = new int[nIntervals];
    for (final KmerAndInterval kmerAndInterval : kmerIntervals) {
        intervalKmerCounts[kmerAndInterval.getIntervalId()] += 1;
    }
    final Set<Integer> intervalsToKill = new HashSet<>();
    final List<AlignedAssemblyOrExcuse> intervalDispositions = new ArrayList<>();
    for (int idx = 0; idx != nIntervals; ++idx) {
        if (intervalKmerCounts[idx] < params.minKmersPerInterval) {
            intervalsToKill.add(idx);
            intervalDispositions.add(new AlignedAssemblyOrExcuse(idx, "FASTQ not written -- too few kmers"));
        }
    }
    qNamesMultiMap.removeIf(qNameAndInterval -> intervalsToKill.contains(qNameAndInterval.getIntervalId()));
    final List<KmerAndInterval> filteredKmerIntervals = kmerIntervals.stream().filter(kmerAndInterval -> !intervalsToKill.contains(kmerAndInterval.getIntervalId())).collect(SVUtils.arrayListCollector(kmerIntervals.size()));
    // record the kmers with their interval IDs
    if (locations.kmerFile != null) {
        try (final OutputStreamWriter writer = new OutputStreamWriter(new BufferedOutputStream(BucketUtils.createFile(locations.kmerFile)))) {
            for (final KmerAndInterval kmerAndInterval : filteredKmerIntervals) {
                writer.write(kmerAndInterval.toString(kSize) + " " + kmerAndInterval.getIntervalId() + "\n");
            }
        } catch (final IOException ioe) {
            throw new GATKException("Can't write kmer intervals file " + locations.kmerFile, ioe);
        }
    }
    return new Tuple2<>(intervalDispositions, filteredKmerIntervals);
}

Example 2 with HopscotchUniqueMultiMap

use of org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMap in project gatk by broadinstitute.

the class FindBreakpointEvidenceSpark method handleAssemblies.

/**
     * Transform all the reads for a supplied set of template names in each interval into FASTQ records
     * for each interval, and do something with the list of FASTQ records for each interval (like write it to a file).
     */
@VisibleForTesting
static List<AlignedAssemblyOrExcuse> handleAssemblies(final JavaSparkContext ctx, final HopscotchUniqueMultiMap<String, Integer, QNameAndInterval> qNamesMultiMap, final JavaRDD<GATKRead> reads, final int nIntervals, final boolean includeMappingLocation, final boolean dumpFASTQs, final LocalAssemblyHandler localAssemblyHandler) {
    final Broadcast<HopscotchUniqueMultiMap<String, Integer, QNameAndInterval>> broadcastQNamesMultiMap = ctx.broadcast(qNamesMultiMap);
    final List<AlignedAssemblyOrExcuse> intervalDispositions = reads.mapPartitionsToPair(readItr -> new ReadsForQNamesFinder(broadcastQNamesMultiMap.value(), nIntervals, includeMappingLocation, dumpFASTQs).call(readItr).iterator(), false).combineByKey(x -> x, FindBreakpointEvidenceSpark::combineLists, FindBreakpointEvidenceSpark::combineLists, new HashPartitioner(nIntervals), false, null).map(localAssemblyHandler::apply).collect();
    broadcastQNamesMultiMap.destroy();
    BwaMemIndexSingleton.closeAllDistributedInstances(ctx);
    return intervalDispositions;
}