Package org.broadinstitute.gatk.engine.resourcemanagement

Examples of org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation

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    private void determineThreadAllocation() {
        if ( argCollection.numberOfDataThreads < 1 ) throw new UserException.BadArgumentValue("num_threads", "cannot be less than 1, but saw " + argCollection.numberOfDataThreads);
        if ( argCollection.numberOfCPUThreadsPerDataThread < 1 ) throw new UserException.BadArgumentValue("num_cpu_threads", "cannot be less than 1, but saw " + argCollection.numberOfCPUThreadsPerDataThread);
        if ( argCollection.numberOfIOThreads < 0 ) throw new UserException.BadArgumentValue("num_io_threads", "cannot be less than 0, but saw " + argCollection.numberOfIOThreads);

        this.threadAllocation = new ThreadAllocation(argCollection.numberOfDataThreads,
                argCollection.numberOfCPUThreadsPerDataThread,
                argCollection.numberOfIOThreads,
                argCollection.monitorThreadEfficiency);
    }
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    }

    /** Test out that we can shard the file and iterate over every read */
    @Test
    public void testUnmappedReadCount() {
        SAMDataSource dataSource = new SAMDataSource(bamList,new ThreadAllocation(),null,genomeLocParser);
        Iterable<Shard> shardStrategy = dataSource.createShardIteratorOverAllReads(new ReadShardBalancer());

        countReadWalker.initialize();
        Object accumulator = countReadWalker.reduceInit();

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    @Test
    public void emptyAlignmentContextTest() {
        SAMRecordIterator iterator = new SAMRecordIterator();

        GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
        Shard shard = new LocusShard(genomeLocParser, new SAMDataSource(Collections.<SAMReaderID>emptyList(),new ThreadAllocation(),null,genomeLocParser),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, null, null);

        LocusView view = createView(dataProvider);
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        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        SAMReaderID readerID = new SAMReaderID(bamFile, new Tags());
        samFiles.add(readerID);

        SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
                false,
                ValidationStringency.STRICT,
                null,
                null,
                new ValidationExclusion(),
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* @version 0.1
*/
public class MockLocusShard extends LocusShard {
    public MockLocusShard(final GenomeLocParser genomeLocParser,final List<GenomeLoc> intervals) {
        super(  genomeLocParser,
                new SAMDataSource(Collections.<SAMReaderID>emptyList(),new ThreadAllocation(),null,genomeLocParser),
                intervals,
                null);
    }
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        public void run() {
            createTestBAM();

            SAMDataSource dataSource = new SAMDataSource(Arrays.asList(testBAM),
                                                         new ThreadAllocation(),
                                                         null,
                                                         new GenomeLocParser(header.getSequenceDictionary()),
                                                         false,
                                                         ValidationStringency.SILENT,
                                                         ReadShard.DEFAULT_MAX_READS,  // reset ReadShard.MAX_READS to ReadShard.DEFAULT_MAX_READS for each test
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Related Classes of org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation

  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard
  • org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSourceUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.FindLargeShards
  • org.broadinstitute.gatk.engine.filters.ReadFilterTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.ReadMetricsUnitTest
  • org.broadinstitute.gatk.engine.traversals.TraverseActiveRegionsUnitTest
  • org.broadinstitute.gatk.engine.traversals.TraverseReadsUnitTest
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