Examples of LocusShard

Examples of org.broadinstitute.gatk.engine.datasources.reads.LocusShard

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    public Iterable<Shard> createShardsOverEntireReference(final SAMDataSource readsDataSource, final GenomeLocParser parser, final int maxShardSize) {
        List<Shard> shards = new ArrayList<Shard>();
        for(SAMSequenceRecord refSequenceRecord: reference.getSequenceDictionary().getSequences()) {
            for(int shardStart = 1; shardStart <= refSequenceRecord.getSequenceLength(); shardStart += maxShardSize) {
                final int shardStop = Math.min(shardStart+maxShardSize-1, refSequenceRecord.getSequenceLength());
                shards.add(new LocusShard(parser,
                        readsDataSource,
                        Collections.singletonList(parser.createGenomeLoc(refSequenceRecord.getSequenceName(),shardStart,shardStop)),
                        null));
            }
        }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.LocusShard

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    public Iterable<Shard> createShardsOverIntervals(final SAMDataSource readsDataSource, final GenomeLocSortedSet intervals, final int maxShardSize) {
        List<Shard> shards = new ArrayList<Shard>();

        for(GenomeLoc interval: intervals) {
            while(interval.size() > maxShardSize) {
                shards.add(new LocusShard(intervals.getGenomeLocParser(),
                        readsDataSource,
                        Collections.singletonList(intervals.getGenomeLocParser().createGenomeLoc(interval.getContig(),interval.getStart(),interval.getStart()+maxShardSize-1)),
                        null));
                interval = intervals.getGenomeLocParser().createGenomeLoc(interval.getContig(),interval.getStart()+maxShardSize,interval.getStop());
            }
            shards.add(new LocusShard(intervals.getGenomeLocParser(),
                    readsDataSource,
                    Collections.singletonList(interval),
                    null));
        }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.LocusShard

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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);

        testReadsInContext(view, shard.getGenomeLocs(), Collections.<GATKSAMRecord>emptyList());
    }
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