Examples with IntervalOverlappingIterator org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator used on opensource projects

Example 1 with IntervalOverlappingIterator

use of org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator in project gatk by broadinstitute.

the class LocusWalker method createAlignmentContextIterator.

private Iterator<AlignmentContext> createAlignmentContextIterator(SAMFileHeader header, LocusIteratorByState libs) {
    Iterator<AlignmentContext> iterator;
    validateEmitEmptyLociParameters();
    if (emitEmptyLoci()) {
        // If no intervals were specified, then use the entire reference (or best available sequence dictionary).
        if (intervalsForTraversal == null) {
            intervalsForTraversal = IntervalUtils.getAllIntervalsForReference(getBestAvailableSequenceDictionary());
        }
        final IntervalLocusIterator intervalLocusIterator = new IntervalLocusIterator(intervalsForTraversal.iterator());
        iterator = new IntervalAlignmentContextIterator(libs, intervalLocusIterator, header.getSequenceDictionary());
    } else {
        // prepare the iterator
        iterator = (hasIntervals()) ? new IntervalOverlappingIterator<>(libs, intervalsForTraversal, header.getSequenceDictionary()) : libs;
    }
    return iterator;
}

Example 2 with IntervalOverlappingIterator

use of org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator in project gatk by broadinstitute.

the class LocusWalkerSpark method getAlignmentsFunction.

/**
     * Return a function that maps a {@link Shard} of reads into a tuple of alignments and their corresponding reference and features.
     * @param bReferenceSource the reference source broadcast
     * @param bFeatureManager the feature manager broadcast
     * @param sequenceDictionary the sequence dictionary for the reads
     * @param header the reads header
     * @param downsamplingInfo the downsampling method for the reads
     * @return a function that maps a {@link Shard} of reads into a tuple of alignments and their corresponding reference and features.
     */
private static FlatMapFunction<Shard<GATKRead>, LocusWalkerContext> getAlignmentsFunction(Broadcast<ReferenceMultiSource> bReferenceSource, Broadcast<FeatureManager> bFeatureManager, SAMSequenceDictionary sequenceDictionary, SAMFileHeader header, LIBSDownsamplingInfo downsamplingInfo) {
    return (FlatMapFunction<Shard<GATKRead>, LocusWalkerContext>) shardedRead -> {
        SimpleInterval interval = shardedRead.getInterval();
        SimpleInterval paddedInterval = shardedRead.getPaddedInterval();
        Iterator<GATKRead> readIterator = shardedRead.iterator();
        ReferenceDataSource reference = bReferenceSource == null ? null : new ReferenceMemorySource(bReferenceSource.getValue().getReferenceBases(null, paddedInterval), sequenceDictionary);
        FeatureManager fm = bFeatureManager == null ? null : bFeatureManager.getValue();
        final Set<String> samples = header.getReadGroups().stream().map(SAMReadGroupRecord::getSample).collect(Collectors.toSet());
        LocusIteratorByState libs = new LocusIteratorByState(readIterator, downsamplingInfo, false, samples, header, true, false);
        IntervalOverlappingIterator<AlignmentContext> alignmentContexts = new IntervalOverlappingIterator<>(libs, ImmutableList.of(interval), sequenceDictionary);
        final Spliterator<AlignmentContext> alignmentContextSpliterator = Spliterators.spliteratorUnknownSize(alignmentContexts, 0);
        return StreamSupport.stream(alignmentContextSpliterator, false).map(alignmentContext -> {
            final SimpleInterval alignmentInterval = new SimpleInterval(alignmentContext);
            return new LocusWalkerContext(alignmentContext, new ReferenceContext(reference, alignmentInterval), new FeatureContext(fm, alignmentInterval));
        }).iterator();
    };
}