Package org.broadinstitute.gatk.engine.executive

Examples of org.broadinstitute.gatk.engine.executive.MicroScheduler


        // initialize sampleDB
        initializeSampleDB();

        // our microscheduler, which is in charge of running everything
        MicroScheduler microScheduler = createMicroscheduler();
        threadEfficiencyMonitor = microScheduler.getThreadEfficiencyMonitor();

        // create temp directories as necessary
        initializeTempDirectory();

        // create the output streams
        initializeOutputStreams(microScheduler.getOutputTracker());

        // Initializing the shard iterator / BAM schedule might take some time, so let the user know vaguely what's going on
        logger.info("Preparing for traversal" +
                    (readsDataSource.getReaderIDs().size() > 0 ? String.format(" over %d BAM files", readsDataSource.getReaderIDs().size()) : ""));
        Iterable<Shard> shardStrategy = getShardStrategy(readsDataSource,microScheduler.getReference(),intervals);
        logger.info("Done preparing for traversal");

        // execute the microscheduler, storing the results
        return microScheduler.execute(this.walker, shardStrategy);

        //monitor.stop();
        //logger.info(String.format("Maximum heap size consumed: %d",monitor.getMaxMemoryUsed()));

        //return result;
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