Package org.broadinstitute.gatk.utils.fasta

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

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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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    public MergeSegregatingAlternateAllelesVCFWriter(VariantContextWriter innerWriter, GenomeLocParser genomeLocParser, File referenceFile, VariantContextMergeRule vcMergeRule, PhasingUtils.AlleleMergeRule alleleMergeRule, String singleSample, boolean emitOnlyMergedRecords, Logger logger, boolean takeOwnershipOfInner, boolean trackAltAlleleStats) {
        this.innerWriter = innerWriter;
        this.genomeLocParser = genomeLocParser;
        try {
            this.referenceFileForMNPmerging = new CachingIndexedFastaSequenceFile(referenceFile);
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
        }       
        this.vcMergeRule = vcMergeRule;
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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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    SAMSequenceDictionary dictForFails;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final GenomeLocParser genomeLocParser = new GenomeLocParser(seq);
        dictForFails = genomeLocParser.getContigs();
    }
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    @DataProvider(name = "MyDataProvider")
    public Object[][] makeMyDataProvider() throws Exception {
        List<Object[]> tests = new ArrayList<Object[]>();

        for ( final String ref : Arrays.asList(b37KGReference, hg18Reference) ) {
            final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(ref));
            final GenomeLocParser genomeLocParser = new GenomeLocParser(seq);
            final SAMSequenceDictionary dict = genomeLocParser.getContigs();

            for ( final SAMSequenceRecord rec1 : dict.getSequences() ) {
                for ( final SAMSequenceRecord rec2 : dict.getSequences() ) {
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            // we don't want to assume that reads will be written in order by the manager because in deep, deep pileups it won't work
            Utils.setupWriter(writer, toolkit, toolkit.getSAMFileHeader(), false, this, PROGRAM_RECORD_NAME);
        }

        try {
            final CachingIndexedFastaSequenceFile referenceReader = new CachingIndexedFastaSequenceFile(toolkit.getArguments().referenceFile);
            overhangManager = new OverhangFixingManager(writer, toolkit.getGenomeLocParser(), referenceReader, MAX_RECORDS_IN_MEMORY, MAX_MISMATCHES_IN_OVERHANG, MAX_BASES_TO_CLIP, doNotFixOverhangs);
        }
        catch (FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(toolkit.getArguments().referenceFile, ex);
        }
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    private SAMFileHeader header;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    }
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    private SAMFileHeader header;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    }
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public class ProgressMeterDaemonUnitTest extends BaseTest {
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));
    }
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    private static final int numReadsPerContig = 250000;
    private static final List<String> contigs = Arrays.asList("1", "2", "3");

    @BeforeClass
    private void init() throws IOException {
        reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        dictionary = reference.getSequenceDictionary();
        genomeLocParser = new GenomeLocParser(dictionary);
        header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
        header.setSequenceDictionary(dictionary);
        header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
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