Examples with VariantFilter org.broadinstitute.hellbender.engine.filters.VariantFilter used on opensource projects

Example 1 with VariantFilter

use of org.broadinstitute.hellbender.engine.filters.VariantFilter in project gatk by broadinstitute.

the class VariantWalkerBase method traverse.

/**
     * Implementation of variant-based traversal.
     * Subclasses can override to provide their own behavior but default implementation should be suitable for most uses.
     */
@Override
public void traverse() {
    final VariantFilter variantfilter = makeVariantFilter();
    final CountingReadFilter readFilter = makeReadFilter();
    // Process each variant in the input stream.
    StreamSupport.stream(getSpliteratorForDrivingVariants(), false).filter(variantfilter).forEach(variant -> {
        final SimpleInterval variantInterval = new SimpleInterval(variant);
        apply(variant, new ReadsContext(reads, variantInterval, readFilter), new ReferenceContext(reference, variantInterval), new FeatureContext(features, variantInterval));
        progressMeter.update(variantInterval);
    });
}

Example 2 with VariantFilter

use of org.broadinstitute.hellbender.engine.filters.VariantFilter in project gatk by broadinstitute.

the class VariantWalkerSpark method getVariants.

/**
     * Loads variants and the corresponding reads, reference and features into a {@link JavaRDD} for the intervals specified.
     * FOr the current implementation the reads context will always be empty.
     *
     * If no intervals were specified, returns all the variants.
     *
     * @return all variants as a {@link JavaRDD}, bounded by intervals if specified.
     */
public JavaRDD<VariantWalkerContext> getVariants(JavaSparkContext ctx) {
    SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
    List<SimpleInterval> intervals = hasIntervals() ? getIntervals() : IntervalUtils.getAllIntervalsForReference(sequenceDictionary);
    // use unpadded shards (padding is only needed for reference bases)
    final List<ShardBoundary> intervalShards = intervals.stream().flatMap(interval -> Shard.divideIntervalIntoShards(interval, variantShardSize, 0, sequenceDictionary).stream()).collect(Collectors.toList());
    JavaRDD<VariantContext> variants = variantsSource.getParallelVariantContexts(drivingVariantFile, getIntervals());
    VariantFilter variantFilter = makeVariantFilter();
    variants = variants.filter(variantFilter::test);
    JavaRDD<Shard<VariantContext>> shardedVariants = SparkSharder.shard(ctx, variants, VariantContext.class, sequenceDictionary, intervalShards, variantShardSize, shuffle);
    Broadcast<ReferenceMultiSource> bReferenceSource = hasReference() ? ctx.broadcast(getReference()) : null;
    Broadcast<FeatureManager> bFeatureManager = features == null ? null : ctx.broadcast(features);
    return shardedVariants.flatMap(getVariantsFunction(bReferenceSource, bFeatureManager, sequenceDictionary, variantShardPadding));
}