Package org.broadinstitute.gatk.engine.refdata

Examples of org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));

        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Arrays.asList(dataSource1,dataSource2));
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );

        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
        TableFeature datum1 = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest1"));

        Assert.assertEquals(datum1.get("COL1"),"C","datum1 parameter for COL1 is incorrect");
        Assert.assertEquals(datum1.get("COL2"),"D","datum1 parameter for COL2 is incorrect");
        Assert.assertEquals(datum1.get("COL3"),"E","datum1 parameter for COL3 is incorrect");

        TableFeature datum2 = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest2"));

        Assert.assertEquals(datum2.get("COL1"),"C","datum2 parameter for COL1 is incorrect");
        Assert.assertEquals(datum2.get("COL2"),"D","datum2 parameter for COL2 is incorrect");
        Assert.assertEquals(datum2.get("COL3"),"E","datum2 parameter for COL3 is incorrect");
    }
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        final IntervalReferenceOrderedView view = new IntervalReferenceOrderedView(genomeLocParser, span, names, iterators);

        if ( testStateless ) {
            // test each tracker is well formed, as each is created
            for ( final GenomeLoc interval : intervals ) {
                final RefMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
                testMetaDataTrackerBindings(tracker, interval, RODs, rodBindings);
            }
        } else {
            // tests all trackers are correct after reading them into an array
            // this checks that the trackers are be safely stored away and analyzed later (critical for nano-scheduling)
            final List<RefMetaDataTracker> trackers = new ArrayList<RefMetaDataTracker>();
            for ( final GenomeLoc interval : intervals ) {
                final RefMetaDataTracker tracker = view.getReferenceOrderedDataForInterval(interval);
                trackers.add(tracker);
            }

            for ( int i = 0; i < trackers.size(); i++) {
                testMetaDataTrackerBindings(trackers.get(i), intervals.get(i), RODs, rodBindings);
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