Examples with FlagStatus org.broadinstitute.hellbender.tools.FlagStat.FlagStatus used on opensource projects

Example 1 with FlagStatus

use of org.broadinstitute.hellbender.tools.FlagStat.FlagStatus in project gatk by broadinstitute.

the class FlagStatSpark method runTool.

@Override
protected void runTool(final JavaSparkContext ctx) {
    final JavaRDD<GATKRead> reads = getReads();
    final FlagStatus result = reads.aggregate(new FlagStatus(), FlagStatus::add, FlagStatus::merge);
    System.out.println(result);
    if (out != null) {
        try (final PrintStream ps = new PrintStream(BucketUtils.createFile(out))) {
            ps.print(result);
        }
    }
}