Examples with BQSRReadTransformer org.broadinstitute.hellbender.transformers.BQSRReadTransformer used on opensource projects

Example 1 with BQSRReadTransformer

use of org.broadinstitute.hellbender.transformers.BQSRReadTransformer in project gatk by broadinstitute.

the class ApplyBQSRSparkFn method apply.

public static JavaRDD<GATKRead> apply(JavaRDD<GATKRead> reads, final Broadcast<RecalibrationReport> reportBroadcast, final SAMFileHeader readsHeader, ApplyBQSRArgumentCollection args) {
    return reads.mapPartitions(readsIterator -> {
        final RecalibrationReport report = reportBroadcast.getValue();
        final BQSRReadTransformer transformer = new BQSRReadTransformer(readsHeader, report, args);
        final Iterable<GATKRead> readsIterable = () -> readsIterator;
        return Utils.stream(readsIterable).map(read -> transformer.apply(read)).collect(Collectors.toList()).iterator();
    });
}