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

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

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//        view.getReferenceContext(shard.getGenomeLoc()).getBase();
//    }

    @Test
    public void testOverlappingReferenceBases() {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(),
                                                                                                                   sequenceFile.getSequence("chrM").length() - 10,
                                                                                                                   sequenceFile.getSequence("chrM").length())));
        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);

        byte[] results = view.getReferenceBases(genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(),
                                                                                sequenceFile.getSequence("chrM").length() - 10,
                                                                                sequenceFile.getSequence("chrM").length() + 9));
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    /** Queries outside the bounds of the shard should result in reference context window trimmed at the shard boundary. */
    @Test
    public void testBoundsFailure() {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(), 1, 50)));

        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);

        GenomeLoc locus = genomeLocParser.createGenomeLoc(sequenceFile.getSequenceDictionary().getSequence(0).getSequenceName(), 50, 51);

        ReferenceContext rc = view.getReferenceContext(locus);
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     * Compares the contents of the fasta and view at a specified location.
     *
     * @param loc
     */
    protected void validateLocation( GenomeLoc loc ) {
        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(loc));
        GenomeLocusIterator shardIterator = new GenomeLocusIterator(genomeLocParser,loc);

        LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, loc, null, sequenceFile, null);
        LocusReferenceView view = new LocusReferenceView(dataProvider);

        while (shardIterator.hasNext()) {
            GenomeLoc locus = shardIterator.next();

            ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
            char expected = Character.toUpperCase(StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0));
            char actual = view.getReferenceContext(locus).getBaseAsChar();

            Assert.assertEquals(actual, expected, String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLocs())
            );
        }
    }
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    public void readsSpanningTest() {
        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);
        testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
    }
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        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 1, 5);
        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);
        testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
    }
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        GATKSAMRecord read2 = buildSAMRecord("read2","chr1", 3, 7);
        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);
        testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
    }
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        GATKSAMRecord read4 = buildSAMRecord("read4","chr1", 4, 8);
        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);
        testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
    }
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        GATKSAMRecord read11 = buildSAMRecord("read11","chr1", 11, 15);
        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,
                           read07, read08, read09, read10, read11, read12);
        testReadsInContext(view, shard.getGenomeLocs(), expectedReads);
    }
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    /**
     * Make sure binding to an empty list produces an empty tracker.
     */
    @Test
    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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    public void testSingleBinding() {
        String fileName = privateTestDir + "TabularDataTest.dat";
        RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,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, 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"));
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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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