Package org.broadinstitute.gatk.engine.refdata.utils

Examples of org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator

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        this.fileDescriptor = fileDescriptor;
        this.builder = builder;
        this.flashbackData = flashbackData;

        // prepopulate one RMDTrack
        LocationAwareSeekableRODIterator iterator = createNewResource();
        this.addNewResource(iterator);

        // Pull the proper header and sequence dictionary from the prepopulated track.
        this.header = iterator.getHeader();
        this.sequenceDictionary = iterator.getSequenceDictionary();
    }
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     */
    public LocationAwareSeekableRODIterator createNewResource() {
        if(numIterators() > 0)
            throw new ReviewedGATKException("BUG: Tried to create multiple iterators over streaming ROD interface");
        RMDTrack track = builder.createInstanceOfTrack(fileDescriptor);
        LocationAwareSeekableRODIterator iter = new SeekableRODIterator(track.getHeader(),track.getSequenceDictionary(),referenceSequenceDictionary,genomeLocParser,track.getIterator());
        return (flashbackData) ? new FlashBackIterator(iter) : iter;
    }
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            if ( DEBUG ) System.out.printf("Shard is %s%n", provider.getLocus());

            // grab the ROD iterator from the data source, and compute the first location in this shard, forwarding
            // the iterator to immediately before it, so that it can be added to the merging iterator primed for
            // next() to return the first real ROD in this shard
            LocationAwareSeekableRODIterator it = dataSource.seek(provider.getLocus());
            it.seekForward(genomeLocParser.createGenomeLoc(loc.getContig(), loc.getStart()-1));

            states.add(new ReferenceOrderedDataState(dataSource,it));           

            // we need to special case the interval so we don't always think there's a rod at the first location
            if ( dataSource.getName().equals(INTERVAL_ROD_NAME) ) {
                if ( interval != null )
                    throw new RuntimeException("BUG: interval local variable already assigned " + interval);
                interval = it.next();
            } else {
                iterators.add( it );
            }
        }
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    }

    private void printGeneStats(List<Pair<GenomeLoc, CoveragePartitioner>> statsByTarget) {
        logger.debug("statsByTarget size is "+Integer.toString(statsByTarget.size()));
        logger.debug("Initializing refseq...");
        LocationAwareSeekableRODIterator refseqIterator = initializeRefSeq();
        logger.debug("Refseq init done.");
        List<Pair<String,DepthOfCoverageStats>> statsByGene = new ArrayList<Pair<String,DepthOfCoverageStats>>();// maintains order
        Map<String,DepthOfCoverageStats> geneNamesToStats = new HashMap<String,DepthOfCoverageStats>(); // allows indirect updating of objects in list

        for ( Pair<GenomeLoc, CoveragePartitioner> targetStats : statsByTarget ) {
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    }

    @Test
    public void testCreateSingleIterator() {
        ResourcePool iteratorPool = new ReferenceOrderedDataPool(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
        LocationAwareSeekableRODIterator iterator = (LocationAwareSeekableRODIterator)iteratorPool.iterator( new MappedStreamSegment(testSite1) );

        Assert.assertEquals(iteratorPool.numIterators(), 1, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");

        TableFeature datum = (TableFeature)iterator.next().get(0).getUnderlyingObject();

        assertTrue(datum.getLocation().equals(testSite1));
        assertTrue(datum.get("COL1").equals("A"));
        assertTrue(datum.get("COL2").equals("B"));
        assertTrue(datum.get("COL3").equals("C"));
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    }

    @Test
    public void testCreateMultipleIterators() {
        ReferenceOrderedQueryDataPool iteratorPool = new ReferenceOrderedQueryDataPool(triplet,builder,seq.getSequenceDictionary(),genomeLocParser);
        LocationAwareSeekableRODIterator iterator1 = iteratorPool.iterator( new MappedStreamSegment(testInterval1) );

        // Create a new iterator at position 2.
        LocationAwareSeekableRODIterator iterator2 = iteratorPool.iterator( new MappedStreamSegment(testInterval2) );

        Assert.assertEquals(iteratorPool.numIterators(), 2, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");

        // Test out-of-order access: first iterator2, then iterator1.
        // Ugh...first call to a region needs to be a seek.
        TableFeature datum = (TableFeature)iterator2.seekForward(testSite2).get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite2));
        assertTrue(datum.get("COL1").equals("C"));
        assertTrue(datum.get("COL2").equals("D"));
        assertTrue(datum.get("COL3").equals("E"));

        datum = (TableFeature)iterator1.next().get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite1));
        assertTrue(datum.get("COL1").equals("A"));
        assertTrue(datum.get("COL2").equals("B"));
        assertTrue(datum.get("COL3").equals("C"));

        // Advance iterator2, and make sure both iterator's contents are still correct.
        datum = (TableFeature)iterator2.next().get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite3));
        assertTrue(datum.get("COL1").equals("F"));
        assertTrue(datum.get("COL2").equals("G"));
        assertTrue(datum.get("COL3").equals("H"));
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    }

    @Test
    public void testIteratorConservation() {
        ReferenceOrderedDataPool iteratorPool = new ReferenceOrderedDataPool(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
        LocationAwareSeekableRODIterator iterator = iteratorPool.iterator( new MappedStreamSegment(testSite1) );

        Assert.assertEquals(iteratorPool.numIterators(), 1, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");

        TableFeature datum = (TableFeature)iterator.next().get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite1));
        assertTrue(datum.get("COL1").equals("A"));
        assertTrue(datum.get("COL2").equals("B"));
        assertTrue(datum.get("COL3").equals("C"));

        iteratorPool.release(iterator);

        // Create another iterator after the current iterator.
        iterator = iteratorPool.iterator( new MappedStreamSegment(testSite3) );

        // Make sure that the previously acquired iterator was reused.
        Assert.assertEquals(iteratorPool.numIterators(), 1, "Number of iterators in the pool is incorrect");
        Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");

        datum = (TableFeature)iterator.seekForward(testSite3).get(0).getUnderlyingObject();
        assertTrue(datum.getLocation().equals(testSite3));
        assertTrue(datum.get("COL1").equals("F"));
        assertTrue(datum.get("COL2").equals("G"));
        assertTrue(datum.get("COL3").equals("H"));
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Related Classes of org.broadinstitute.gatk.engine.refdata.utils.LocationAwareSeekableRODIterator

  • org.broadinstitute.gatk.engine.datasources.providers.RodLocusView
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPool
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPoolUnitTest
  • org.broadinstitute.gatk.tools.walkers.coverage.DepthOfCoverage
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