Package org.broadinstitute.gatk.utils.fasta

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

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     * Called before every test case method.
     */
    @BeforeMethod
    public void doForEachTest() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary());
    }
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    @BeforeMethod
    public void doForEachTest() throws FileNotFoundException {
        readers = new ArrayList<SAMReaderID>();

        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b36KGReference));
        genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary());
    }
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    @BeforeMethod
    public void setup() {
        File referenceFile = new File(b36KGReference);
        try {
            IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(referenceFile);
            genomeLocParser = new GenomeLocParser(seq);
            manager = new FeatureManager();
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
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public class FeatureToGATKFeatureIteratorUnitTest extends BaseTest {
    @Test
    @SuppressWarnings("unchecked")
    public void testCloseFilePointers() throws IOException {
        final String chr = "20";
        IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
        GenomeLocParser parser = new GenomeLocParser(seq);
        File file = new File(privateTestDir + "NA12878.hg19.example1.vcf");
        VCFCodec codec = new VCFCodec();
        TestFeatureReader reader = new TestFeatureReader(file.getAbsolutePath(), codec);
        CheckableCloseableTribbleIterator<Feature> tribbleIterator = reader.query(chr, 1, 100000);
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    @BeforeMethod
    public void setup() {
        File referenceFile = new File(b37KGReference);
        try {
            seq = new CachingIndexedFastaSequenceFile(referenceFile);
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
        }
        genomeLocParser = new GenomeLocParser(seq);
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    private int contigLength;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
        contig = "1";
        contigLength = genomeLocParser.getContigInfo(contig).getSequenceLength();
    }
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    private final static double ACTIVE_PROB_THRESHOLD= 0.002;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
    }
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    private final static double ACTIVE_PROB_THRESHOLD= 0.002;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq);
        startLoc = genomeLocParser.createGenomeLoc("chr1", 1, 1, 100);
    }
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            throw new UserException.MissingReferenceDictFile(dictFile, fastaFile);
        }

        // Read reference data by creating an IndexedFastaSequenceFile.
        try {
            reference = new CachingIndexedFastaSequenceFile(fastaFile);
        }
        catch (IllegalArgumentException e) {
            throw new UserException.CouldNotReadInputFile(fastaFile, "Could not read reference sequence.  The FASTA must have either a .fasta or .fa extension", e);
        }
        catch (Exception e) {
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        File hg18Ref = new File(BaseTest.hg18Reference);
        try {
            ReferenceDataSource referenceDataSource = new ReferenceDataSource(hg18Ref);
            hg18Header = new SAMFileHeader();
            hg18Header.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary());
            ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg18Ref);
            hg18GenomeLocParser = new GenomeLocParser(seq);
            hg18ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ;
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(hg18Ref,ex);
        }

        File hg19Ref = new File(BaseTest.hg19Reference);
        try {
            ReferenceDataSource referenceDataSource = new ReferenceDataSource(hg19Ref);
            hg19Header = new SAMFileHeader();
            hg19Header.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary());
            ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg19Ref);
            hg19GenomeLocParser = new GenomeLocParser(seq);
            hg19ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ;

            hg19exomeIntervals = Collections.unmodifiableList(IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(hg19Intervals)));
        }
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