Package org.broadinstitute.gatk.engine.refdata

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

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    }

    private void initialize(StratifiedEvalTestProvider cfg) {
        VEwalker.createStratificationStates(cfg.stratificationObjects, cfg.evaluationObjects);

        final RefMetaDataTracker tracker = new RefMetaDataTracker();
        final ReferenceContext ref = null;
        final VariantContext comp = null;
        final String compName = null, sampleName = null;

        // increment eval counts for each stratification of divisors of i from from 1...maxI
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                    activeRegion.getLocation(), activeRegion.getLocation().size(), activeRegion.isActive(), activeRegion.size(), maxReadsInMemory));

        // prepare the RefMetaDataTracker information
        final GenomeLoc loc = activeRegion.getLocation();
        // get all of the RODs that cover the active region (without extension)
        final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataForInterval(loc);
        // trim away all of the features that occurred before this location, as we will not need them in the future
        referenceOrderedDataView.trimCurrentFeaturesToLoc(loc);

        return new MapData(activeRegion, tracker);
    }
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                    // create reference context. Note that if we have a pileup of "extended events", the context will
                    // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup).
                    final ReferenceContext refContext = referenceView.getReferenceContext(location);

                    // Iterate forward to get all reference ordered data covering this location
                    final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation());

                    // Call the walkers isActive function for this locus and add them to the list to be integrated later
                    addIsActiveResult(walker, tracker, refContext, locus);

                    maxReadsInMemory = Math.max(myReads.size(), maxReadsInMemory);
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            // create reference context. Note that if we have a pileup of "extended events", the context will
            // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup).
            final ReferenceContext refContext = referenceView.getReferenceContext(location);

            // Iterate forward to get all reference ordered data covering this location
            final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(location);

            numIterations++;
            return new MapData(locus, refContext,  tracker);
        }
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                final ReferenceContext refContext = ! read.getReadUnmappedFlag()
                        ? reference.getReferenceContext(read)
                        : null;

                // if the read is mapped, create a metadata tracker
                final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0
                        ? rodView.getReferenceOrderedDataForRead(read)
                        : null;

                // update the number of reads we've seen
                dataProvider.getShard().getReadMetrics().incrementNumIterations();
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            for ( ReferenceOrderedDataState state: states )
                // todo -- warning, I removed the reference to the name from states
                bindings.add( state.iterator.seekForward(loc) );

            return new RefMetaDataTracker(bindings);
        }
    }
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            return RefMetaDataTracker.EMPTY_TRACKER;
        else {
            final List<RODRecordList> bindings = new ArrayList<>(states.size());
            for ( final RMDDataState state : states )
                bindings.add(state.stream.getOverlapping(interval));
            return new RefMetaDataTracker(bindings);
        }
    }
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    @Override
    public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc ) {
        // special case the interval again -- add it into the ROD
        if ( interval != null ) { allTracksHere.add(interval); }
        return new RefMetaDataTracker(allTracksHere);
    }
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    public void testNoBindings() {
        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, Collections.<ReferenceOrderedDataSource>emptyList());
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );

        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10));
        Assert.assertEquals(tracker.getValues(Feature.class).size(), 0, "The tracker should not have produced any data");
    }
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        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, Collections.singletonList(dataSource));
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );

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

        Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect");
        Assert.assertEquals(datum.get("COL2"),"D","datum parameter for COL2 is incorrect");
        Assert.assertEquals(datum.get("COL3"),"E","datum parameter for COL3 is incorrect");
    }
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Related Classes of org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker

  • org.broadinstitute.gatk.engine.datasources.providers.IntervalReferenceOrderedView
  • org.broadinstitute.gatk.engine.datasources.providers.IntervalReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ManagingReferenceOrderedView
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.RodLocusView
  • org.broadinstitute.gatk.engine.refdata.utils.RODRecordList
  • org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions
  • org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator
  • org.broadinstitute.gatk.engine.traversals.TraverseLociNano$MapDataIterator
  • org.broadinstitute.gatk.engine.traversals.TraverseReadsNano
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