Examples with ReadContextData org.broadinstitute.hellbender.engine.ReadContextData used on opensource projects

Example 6 with ReadContextData

use of org.broadinstitute.hellbender.engine.ReadContextData in project gatk by broadinstitute.

the class BQSRPipelineSpark method runTool.

@Override
protected void runTool(final JavaSparkContext ctx) {
    if (joinStrategy == JoinStrategy.BROADCAST && !getReference().isCompatibleWithSparkBroadcast()) {
        throw new UserException.Require2BitReferenceForBroadcast();
    }
    //Should this get the getUnfilteredReads? getReads will merge default and command line filters.
    //but the code below uses other filters for other parts of the pipeline that do not honor
    //the commandline.
    final JavaRDD<GATKRead> initialReads = getReads();
    // The initial reads have already had the WellformedReadFilter applied to them, which
    // is all the filtering that ApplyBQSR wants. BQSR itself wants additional filtering
    // performed, so we do that here.
    //NOTE: this filter doesn't honor enabled/disabled commandline filters
    final ReadFilter bqsrReadFilter = ReadFilter.fromList(BaseRecalibrator.getBQSRSpecificReadFilterList(), getHeaderForReads());
    final JavaRDD<GATKRead> filteredReadsForBQSR = initialReads.filter(read -> bqsrReadFilter.test(read));
    final VariantsSparkSource variantsSparkSource = new VariantsSparkSource(ctx);
    final JavaRDD<GATKVariant> bqsrKnownVariants = variantsSparkSource.getParallelVariants(baseRecalibrationKnownVariants, getIntervals());
    final JavaPairRDD<GATKRead, ReadContextData> rddReadContext = AddContextDataToReadSpark.add(ctx, filteredReadsForBQSR, getReference(), bqsrKnownVariants, joinStrategy, getReferenceSequenceDictionary(), readShardSize, readShardPadding);
    //note: we use the reference dictionary from the reads themselves.
    final RecalibrationReport bqsrReport = BaseRecalibratorSparkFn.apply(rddReadContext, getHeaderForReads(), getHeaderForReads().getSequenceDictionary(), bqsrArgs);
    final Broadcast<RecalibrationReport> reportBroadcast = ctx.broadcast(bqsrReport);
    final JavaRDD<GATKRead> finalReads = ApplyBQSRSparkFn.apply(initialReads, reportBroadcast, getHeaderForReads(), applyBqsrArgs.toApplyBQSRArgumentCollection(bqsrArgs.PRESERVE_QSCORES_LESS_THAN));
    writeReads(ctx, output, finalReads);
}

Example 7 with ReadContextData

use of org.broadinstitute.hellbender.engine.ReadContextData in project gatk by broadinstitute.

the class AddContextDataToReadSpark method addUsingOverlapsPartitioning.

/**
     * Add context data ({@link ReadContextData}) to reads, using overlaps partitioning to avoid a shuffle.
     * @param ctx the Spark context
     * @param mappedReads the coordinate-sorted reads
     * @param referenceSource the reference source
     * @param variants the coordinate-sorted variants
     * @param sequenceDictionary the sequence dictionary for the reads
     * @param shardSize the maximum size of each shard, in bases
     * @param shardPadding amount of extra context around each shard, in bases
     * @return a RDD of read-context pairs, in coordinate-sorted order
     */
private static JavaPairRDD<GATKRead, ReadContextData> addUsingOverlapsPartitioning(final JavaSparkContext ctx, final JavaRDD<GATKRead> mappedReads, final ReferenceMultiSource referenceSource, final JavaRDD<GATKVariant> variants, final SAMSequenceDictionary sequenceDictionary, final int shardSize, final int shardPadding) {
    final List<SimpleInterval> intervals = IntervalUtils.getAllIntervalsForReference(sequenceDictionary);
    // use unpadded shards (padding is only needed for reference bases)
    final List<ShardBoundary> intervalShards = intervals.stream().flatMap(interval -> Shard.divideIntervalIntoShards(interval, shardSize, 0, sequenceDictionary).stream()).collect(Collectors.toList());
    final Broadcast<ReferenceMultiSource> bReferenceSource = ctx.broadcast(referenceSource);
    final IntervalsSkipList<GATKVariant> variantSkipList = new IntervalsSkipList<>(variants.collect());
    final Broadcast<IntervalsSkipList<GATKVariant>> variantsBroadcast = ctx.broadcast(variantSkipList);
    int maxLocatableSize = Math.min(shardSize, shardPadding);
    JavaRDD<Shard<GATKRead>> shardedReads = SparkSharder.shard(ctx, mappedReads, GATKRead.class, sequenceDictionary, intervalShards, maxLocatableSize);
    return shardedReads.flatMapToPair(new PairFlatMapFunction<Shard<GATKRead>, GATKRead, ReadContextData>() {

        private static final long serialVersionUID = 1L;

        @Override
        public Iterator<Tuple2<GATKRead, ReadContextData>> call(Shard<GATKRead> shard) throws Exception {
            // get reference bases for this shard (padded)
            SimpleInterval paddedInterval = shard.getInterval().expandWithinContig(shardPadding, sequenceDictionary);
            ReferenceBases referenceBases = bReferenceSource.getValue().getReferenceBases(null, paddedInterval);
            final IntervalsSkipList<GATKVariant> intervalsSkipList = variantsBroadcast.getValue();
            Iterator<Tuple2<GATKRead, ReadContextData>> transform = Iterators.transform(shard.iterator(), new Function<GATKRead, Tuple2<GATKRead, ReadContextData>>() {

                @Nullable
                @Override
                public Tuple2<GATKRead, ReadContextData> apply(@Nullable GATKRead r) {
                    List<GATKVariant> overlappingVariants;
                    if (SimpleInterval.isValid(r.getContig(), r.getStart(), r.getEnd())) {
                        overlappingVariants = intervalsSkipList.getOverlapping(new SimpleInterval(r));
                    } else {
                        //Sometimes we have reads that do not form valid intervals (reads that do not consume any ref bases, eg CIGAR 61S90I
                        //In those cases, we'll just say that nothing overlaps the read
                        overlappingVariants = Collections.emptyList();
                    }
                    return new Tuple2<>(r, new ReadContextData(referenceBases, overlappingVariants));
                }
            });
            // only include reads that start in the shard
            return Iterators.filter(transform, r -> r._1().getStart() >= shard.getStart() && r._1().getStart() <= shard.getEnd());
        }
    });
}