Examples of org.broadinstitute.gatk.engine.executive.WindowMaker$WindowMakerIterator

Package org.broadinstitute.gatk.engine.executive

Examples of org.broadinstitute.gatk.engine.executive.WindowMaker$WindowMakerIterator

org.broadinstitute.gatk.engine.executive.WindowMaker
Transforms an iterator of reads which overlap the given interval list into an iterator of covered single-base loci completely contained within the interval list. To do this, it creates a LocusIteratorByState which will emit a single-bp locus for every base covered by the read iterator, then uses the WindowMakerIterator.advance() to filter down that stream of loci to only those covered by the given interval list. Example: Incoming stream of reads: A:chr20:1-5, B:chr20:2-6, C:chr20:2-7, D:chr20:3-8, E:chr20:5-10 Incoming intervals: chr20:3-7 Locus iterator by state will produce the following stream of data: chr1:1 {A}, chr1:2 {A,B,C}, chr1:3 {A,B,C,D}, chr1:4 {A,B,C,D}, chr1:5 {A,B,C,D,E}, chr1:6 {B,C,D,E}, chr1:7 {C,D,E}, chr1:8 {D,E}, chr1:9 {E}, chr1:10 {E} WindowMakerIterator will then filter the incoming stream, emitting the following stream: chr1:3 {A,B,C,D}, chr1:4 {A,B,C,D}, chr1:5 {A,B,C,D,E}, chr1:6 {B,C,D,E}, chr1:7 {C,D,E} @author mhanna @version 0.1

        final TraverseLociNano traverseLociNano = new TraverseLociNano(1);
        final DummyLocusWalker walker = new DummyLocusWalker();
        traverseLociNano.initialize(engine, walker, null);


        for ( final Shard shard : dataSource.createShardIteratorOverAllReads(new LocusShardBalancer()) ) {
            final WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples);
            for ( WindowMaker.WindowMakerIterator window : windowMaker ) {
                final LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
                traverseLociNano.traverse(walker, dataProvider, 0);
                dataProvider.close();
            }
            windowMaker.close();
        }


        //dataSource.close();
        Assert.assertEquals(engine.getCumulativeMetrics().getNumReadsSeen(), contigs.size() * numReadsPerContig);
        Assert.assertEquals(engine.getCumulativeMetrics().getNumIterations(), contigs.size() * numReadsPerContig);

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        final TraverseActiveRegions traverseActiveRegions = new TraverseActiveRegions();
        final DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
        traverseActiveRegions.initialize(engine, walker, null);


        for ( final Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new ActiveRegionShardBalancer()) ) {
            final WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples);
            for ( WindowMaker.WindowMakerIterator window : windowMaker ) {
                final LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
                traverseActiveRegions.traverse(walker, dataProvider, 0);
                dataProvider.close();
            }
            windowMaker.close();
        }


        Assert.assertEquals(engine.getCumulativeMetrics().getNumReadsSeen(), contigs.size() * numReadsPerContig);
        Assert.assertEquals(engine.getCumulativeMetrics().getNumIterations(), contigs.size() * numReadsPerContig);
    }

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    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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        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(shardBounds));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);


        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));

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    public void readCoveringFirstPartTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

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    public void readCoveringLastPartTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 6, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

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    public void readCoveringMiddleTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 3, 7);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

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    public void readAndLocusOverlapAtLastBase() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 5);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 5, 5)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

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    public void readOverlappingStartTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 1, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

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    public void readOverlappingEndTest() {
        GATKSAMRecord read = buildSAMRecord("read1","chr1", 6, 15);
        SAMRecordIterator iterator = new SAMRecordIterator(read);


        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
        WindowMaker.WindowMakerIterator window = windowMaker.next();
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
        LocusView view = createView(dataProvider);


        testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
    }

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org.broadinstitute.gatk.engine.ReadMetricsUnitTest

org.broadinstitute.gatk.engine.traversals.TraverseActiveRegionsUnitTest

org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState

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