Examples with ReferenceMultiSource org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource used on opensource projects

Example 11 with ReferenceMultiSource

use of org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource in project gatk by broadinstitute.

the class PathSeqFilterSpark method doHostBWA.

private JavaRDD<GATKRead> doHostBWA(final JavaSparkContext ctx, final SAMFileHeader readsHeader, final JavaRDD<GATKRead> reads) {
    final BwaSparkEngine engine = new BwaSparkEngine(ctx, indexImageFile, getHeaderForReads(), getReferenceSequenceDictionary());
    // null if we have no api key
    final GCSOptions gcsOptions = getAuthenticatedGCSOptions();
    final ReferenceMultiSource hostReference = new ReferenceMultiSource(gcsOptions, HOST_REF_PATH, getReferenceWindowFunction());
    final SAMSequenceDictionary hostRefDict = hostReference.getReferenceSequenceDictionary(header.getSequenceDictionary());
    readsHeader.setSequenceDictionary(hostRefDict);
    return engine.align(reads);
}

Example 12 with ReferenceMultiSource

use of org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource in project gatk-protected by broadinstitute.

the class HaplotypeCallerSparkIntegrationTest method testReferenceAdapterIsSerializable.

@Test
public void testReferenceAdapterIsSerializable() throws IOException {
    final AuthHolder auth = new AuthHolder("name", "somestring");
    final ReferenceMultiSource referenceMultiSource = new ReferenceMultiSource(auth, b37_2bit_reference_20_21, ReferenceWindowFunctions.IDENTITY_FUNCTION);
    SparkTestUtils.roundTripInKryo(referenceMultiSource, ReferenceMultiSource.class, SparkContextFactory.getTestSparkContext().getConf());
    final HaplotypeCallerSpark.ReferenceMultiSourceAdapter adapter = new HaplotypeCallerSpark.ReferenceMultiSourceAdapter(referenceMultiSource, auth);
    SparkTestUtils.roundTripInKryo(adapter, HaplotypeCallerSpark.ReferenceMultiSourceAdapter.class, SparkContextFactory.getTestSparkContext().getConf());
}

Example 13 with ReferenceMultiSource

use of org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource in project gatk by broadinstitute.

the class GATKSparkTool method initializeReference.

/**
     * Initializes our reference source. Does nothing if no reference was specified.
     */
private void initializeReference() {
    // null if we have no api key
    final GCSOptions gcsOptions = getAuthenticatedGCSOptions();
    final String referenceURL = referenceArguments.getReferenceFileName();
    if (referenceURL != null) {
        referenceSource = new ReferenceMultiSource(gcsOptions, referenceURL, getReferenceWindowFunction());
        referenceDictionary = referenceSource.getReferenceSequenceDictionary(readsHeader != null ? readsHeader.getSequenceDictionary() : null);
        if (referenceDictionary == null) {
            throw new UserException.MissingReferenceDictFile(referenceURL);
        }
    }
}

Example 14 with ReferenceMultiSource

use of org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource in project gatk by broadinstitute.

the class LocusWalkerSpark method getAlignments.

/**
     * Loads alignments and the corresponding reference and features into a {@link JavaRDD} for the intervals specified.
     *
     * If no intervals were specified, returns all the alignments.
     *
     * @return all alignments as a {@link JavaRDD}, bounded by intervals if specified.
     */
public JavaRDD<LocusWalkerContext> getAlignments(JavaSparkContext ctx) {
    SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
    List<SimpleInterval> intervals = hasIntervals() ? getIntervals() : IntervalUtils.getAllIntervalsForReference(sequenceDictionary);
    final List<ShardBoundary> intervalShards = intervals.stream().flatMap(interval -> Shard.divideIntervalIntoShards(interval, readShardSize, readShardPadding, sequenceDictionary).stream()).collect(Collectors.toList());
    int maxLocatableSize = Math.min(readShardSize, readShardPadding);
    JavaRDD<Shard<GATKRead>> shardedReads = SparkSharder.shard(ctx, getReads(), GATKRead.class, sequenceDictionary, intervalShards, maxLocatableSize, shuffle);
    Broadcast<ReferenceMultiSource> bReferenceSource = hasReference() ? ctx.broadcast(getReference()) : null;
    Broadcast<FeatureManager> bFeatureManager = features == null ? null : ctx.broadcast(features);
    return shardedReads.flatMap(getAlignmentsFunction(bReferenceSource, bFeatureManager, sequenceDictionary, getHeaderForReads(), getDownsamplingInfo()));
}

Example 15 with ReferenceMultiSource

use of org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource in project gatk by broadinstitute.

the class VariantWalkerSpark method getVariantsFunction.

private static FlatMapFunction<Shard<VariantContext>, VariantWalkerContext> getVariantsFunction(final Broadcast<ReferenceMultiSource> bReferenceSource, final Broadcast<FeatureManager> bFeatureManager, final SAMSequenceDictionary sequenceDictionary, final int variantShardPadding) {
    return (FlatMapFunction<Shard<VariantContext>, VariantWalkerContext>) shard -> {
        SimpleInterval paddedInterval = shard.getInterval().expandWithinContig(variantShardPadding, sequenceDictionary);
        ReferenceDataSource reference = bReferenceSource == null ? null : new ReferenceMemorySource(bReferenceSource.getValue().getReferenceBases(null, paddedInterval), sequenceDictionary);
        FeatureManager features = bFeatureManager == null ? null : bFeatureManager.getValue();
        return StreamSupport.stream(shard.spliterator(), false).filter(v -> v.getStart() >= shard.getStart() && v.getStart() <= shard.getEnd()).map(v -> {
            final SimpleInterval variantInterval = new SimpleInterval(v);
            return new VariantWalkerContext(v, new ReadsContext(), new ReferenceContext(reference, variantInterval), new FeatureContext(features, variantInterval));
        }).iterator();
    };
}