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

Example 6 with CountingReadFilter

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

the class AssemblyRegionWalker method traverse.

@Override
public final void traverse() {
    CountingReadFilter countedFilter = makeReadFilter();
    // Since we're processing regions rather than individual reads, tell the progress
    // meter to check the time more frequently (every 10 regions instead of every 1000 regions).
    progressMeter.setRecordsBetweenTimeChecks(10L);
    for (final LocalReadShard readShard : readShards) {
        // Since reads in each shard are lazily fetched, we need to pass the filter to the window
        // instead of filtering the reads directly here
        readShard.setReadFilter(countedFilter);
        readShard.setDownsampler(maxReadsPerAlignmentStart > 0 ? new PositionalDownsampler(maxReadsPerAlignmentStart, getHeaderForReads()) : null);
        currentReadShard = readShard;
        processReadShard(readShard, // use the fully-padded window to fetch overlapping data
        new ReferenceContext(reference, readShard.getPaddedInterval()), new FeatureContext(features, readShard.getPaddedInterval()));
    }
    logger.info(countedFilter.getSummaryLine());
}

Example 7 with CountingReadFilter

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

the class FeatureWalker method traverse.

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