Examples with RecalibrationReport org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport used on opensource projects

Example 6 with RecalibrationReport

use of org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport in project gatk by broadinstitute.

the class BQSRPipelineSpark method runTool.

@Override
protected void runTool(final JavaSparkContext ctx) {
    if (joinStrategy == JoinStrategy.BROADCAST && !getReference().isCompatibleWithSparkBroadcast()) {
        throw new UserException.Require2BitReferenceForBroadcast();
    }
    //Should this get the getUnfilteredReads? getReads will merge default and command line filters.
    //but the code below uses other filters for other parts of the pipeline that do not honor
    //the commandline.
    final JavaRDD<GATKRead> initialReads = getReads();
    // The initial reads have already had the WellformedReadFilter applied to them, which
    // is all the filtering that ApplyBQSR wants. BQSR itself wants additional filtering
    // performed, so we do that here.
    //NOTE: this filter doesn't honor enabled/disabled commandline filters
    final ReadFilter bqsrReadFilter = ReadFilter.fromList(BaseRecalibrator.getBQSRSpecificReadFilterList(), getHeaderForReads());
    final JavaRDD<GATKRead> filteredReadsForBQSR = initialReads.filter(read -> bqsrReadFilter.test(read));
    final VariantsSparkSource variantsSparkSource = new VariantsSparkSource(ctx);
    final JavaRDD<GATKVariant> bqsrKnownVariants = variantsSparkSource.getParallelVariants(baseRecalibrationKnownVariants, getIntervals());
    final JavaPairRDD<GATKRead, ReadContextData> rddReadContext = AddContextDataToReadSpark.add(ctx, filteredReadsForBQSR, getReference(), bqsrKnownVariants, joinStrategy, getReferenceSequenceDictionary(), readShardSize, readShardPadding);
    //note: we use the reference dictionary from the reads themselves.
    final RecalibrationReport bqsrReport = BaseRecalibratorSparkFn.apply(rddReadContext, getHeaderForReads(), getHeaderForReads().getSequenceDictionary(), bqsrArgs);
    final Broadcast<RecalibrationReport> reportBroadcast = ctx.broadcast(bqsrReport);
    final JavaRDD<GATKRead> finalReads = ApplyBQSRSparkFn.apply(initialReads, reportBroadcast, getHeaderForReads(), applyBqsrArgs.toApplyBQSRArgumentCollection(bqsrArgs.PRESERVE_QSCORES_LESS_THAN));
    writeReads(ctx, output, finalReads);
}