Package org.broadinstitute.gatk.engine.datasources.reads

Examples of org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard

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        ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(testTriplet1,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        RMDTriplet testTriplet2 = new RMDTriplet("tableTest2","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(testTriplet2,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        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"));
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    public void singleReadTest() {
        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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    @Test
    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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    @Test
    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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    @Test
    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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    @Test
    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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    @Test
    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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    @Test
    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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Related Classes of org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard

  • org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource
  • org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation
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