Package org.broadinstitute.gatk.utils.fasta

Examples of org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile$Cache

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    }

    @Test(expectedExceptions=UserException.BadArgumentValue.class)
    public void testExceptionUponLegacyIntervalSyntax() throws Exception {
        GenomeAnalysisEngine toolkit = new GenomeAnalysisEngine();
        toolkit.setGenomeLocParser(new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference))));

        // Attempting to use the legacy -L "interval1;interval2" syntax should produce an exception:
        IntervalBinding<Feature> binding = new IntervalBinding<Feature>("1;2");
        binding.getIntervals(toolkit);
    }
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    }

    @Test (enabled = true)
    public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException {

        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final int readLength = 76;

        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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    }

    @Test (enabled = true)
    public void testReadWithNsRefAfterDeletion() throws FileNotFoundException {

        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final int readLength = 76;

        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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    @Param({"true", "false"})
    boolean useContigIndex; // set automatically by framework

    @Override protected void setUp() throws Exception {
        seq = new CachingIndexedFastaSequenceFile(new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta"));
    }
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    private IndexedFastaSequenceFile seq;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
    }
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    private static SAMSequenceDictionary dict;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        dict = seq.getSequenceDictionary();
    }
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        ATCATC = Allele.create("ATCATC");
        ATCATCT = Allele.create("ATCATCT");
        ATref = Allele.create("AT",true);
        Anoref = Allele.create("A",false);
        GT = Allele.create("GT",false);
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(hg18Reference)));
    }
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    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq);
    }
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    private IndexedFastaSequenceFile seq;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
    }
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    //
    // -----------------------------------------------------------------------------------------------

    @DataProvider(name = "GetOverlapping")
    public Object[][] makeGetOverlappingTest() throws Exception {
        final GenomeLocParser genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));

        List<Object[]> tests = new ArrayList<Object[]>();

        final GenomeLoc prev1 = genomeLocParser.createGenomeLoc("19", 1, 10);
        final GenomeLoc prev2 = genomeLocParser.createGenomeLoc("19", 20, 50);
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