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

Package org.broadinstitute.gatk.engine.executive

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

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

        GATKSAMRecord read1 = buildSAMRecord("read1","chr1", 1, 5);
        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 6, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);


        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);


        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
        Collections.addAll(expectedReads, read1, read2);

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        GATKSAMRecord read3 = buildSAMRecord("read3","chr1", 6, 10);
        GATKSAMRecord read4 = buildSAMRecord("read4","chr1", 6, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);


        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);


        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
        Collections.addAll(expectedReads, read1, read2, read3, read4);

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        GATKSAMRecord read3 = buildSAMRecord("read3","chr1", 4, 8);
        GATKSAMRecord read4 = buildSAMRecord("read4","chr1", 5, 9);
        SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);


        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);


        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
        Collections.addAll(expectedReads, read1, read2, read3, read4);

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        GATKSAMRecord read5 = buildSAMRecord("read5","chr1", 5, 9);
        GATKSAMRecord read6 = buildSAMRecord("read6","chr1", 6, 10);
        SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);


        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);


        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
        Collections.addAll(expectedReads, read1, read2, read3, read4, read5, read6);

View Full Code Here

        GATKSAMRecord read12 = buildSAMRecord("read12","chr1", 12, 16);
        SAMRecordIterator iterator = new SAMRecordIterator(read01, read02, read03, read04, read05, read06,
                                                           read07, read08, read09, read10, read11, read12);


        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);


        List<GATKSAMRecord> expectedReads = new ArrayList<GATKSAMRecord>();
        Collections.addAll(expectedReads, read01, read02, read03, read04, read05, read06,

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        final Set<String> samples = SampleUtils.getSAMFileSamples(dataSource.getHeader());


        traverseActiveRegions.initialize(engine, walker);
        List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();
        for (Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new ActiveRegionShardBalancer())) {
            for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples)) {
                providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
            }
        }


        return providers;

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org.broadinstitute.gatk.engine.contexts.AlignmentContext

org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate

org.broadinstitute.gatk.engine.iterators.GATKSAMRecordIterator

org.broadinstitute.gatk.engine.ReadMetricsUnitTest

org.broadinstitute.gatk.engine.traversals.TraverseActiveRegionsUnitTest

org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState

java.util.NoSuchElementException

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

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