Package org.broadinstitute.gatk.utils.fasta

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

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        vcfWriter.writeHeader(new VCFHeader(headerInfo, sampleSet));

        try {
            // fasta reference reader to supplement the edges of the reference sequence
            referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
        } catch( FileNotFoundException e ) {
            throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile, e);
        }

        // create and setup the assembler
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        final List<Integer> startsToUse = new LinkedList<Integer>();

        for ( int i = 3; i < args.length; i++ )
            startsToUse.add(Integer.valueOf(args[i]));

        final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(ref);
        final GenomeLocParser parser = new GenomeLocParser(seq);
        final BufferedReader reader = new BufferedReader(new FileReader(exactLogFile));
        final List<ExactCallLogger.ExactCall> loggedCalls = ExactCallLogger.readExactLog(reader, startsToUse, parser);

        for ( final ExactCallLogger.ExactCall call : loggedCalls ) {
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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 CachingIndexedFastaSequenceFile referenceReader;
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        referenceReader = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(referenceReader.getSequenceDictionary());
    }
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    private CachingIndexedFastaSequenceFile referenceReader;
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        referenceReader = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(referenceReader.getSequenceDictionary());
    }
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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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            throw new RuntimeException("LOD threshold cannot be a negative number");
        if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )
            throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1");

        try {
            referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex);
        }
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    LDMerger merger;
    GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));
    }
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    private IndexedFastaSequenceFile seq;
    private SAMFileHeader header;

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

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