Package htsjdk.samtools.reference

Examples of htsjdk.samtools.reference.ReferenceSequenceFile.nextSequence()

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*/
public class CreateBWTFromReference {
    private byte[] loadReference( File inputFile ) {
        // Read in the first sequence in the input file
        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(inputFile);
        ReferenceSequence sequence = reference.nextSequence();
        return sequence.getBases();
    }

    private byte[] loadReverseReference( File inputFile ) {
        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(inputFile);
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        return sequence.getBases();
    }

    private byte[] loadReverseReference( File inputFile ) {
        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(inputFile);
        ReferenceSequence sequence = reference.nextSequence();
        PackUtils.reverse(sequence.getBases());
        return sequence.getBases();
    }

    private Counts countOccurrences( byte[] sequence ) {
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        // Read in the first sequence in the input file
        String inputFileName = argv[0];
        File inputFile = new File(inputFileName);
        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(inputFile);
        ReferenceSequence sequence = reference.nextSequence();

        // Target file for output
        PackUtils.writeReferenceSequence( new File(argv[1]), sequence.getBases() );

        // Reverse the bases in the reference
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        if (clipSequenceFile != null) {
            ReferenceSequenceFile rsf = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(clipSequenceFile));

            while (true) {
                ReferenceSequence rs = rsf.nextSequence();
                if (rs == null)
                    break;
                else {
                    addSeqToClip(rs.getName(), rs.getBases());
                }
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        // Loop over the reference and the reads and calculate the basic metrics
        ////////////////////////////////////////////////////////////////////////////
        ReferenceSequence ref = null;
        final ProgressLogger
                progress = new ProgressLogger(log);
        while ((ref = referenceFile.nextSequence()) != null) {
            final byte[] refBases = ref.getBases();
            StringUtil.toUpperCase(refBases);
            final int refLength = refBases.length;
            final int lastWindowStart = refLength - WINDOW_SIZE;
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        final ReferenceSequenceFile refSeqFile =
                ReferenceSequenceFileFactory.getReferenceSequenceFile(referenceFile, TRUNCATE_NAMES_AT_WHITESPACE);
        ReferenceSequence refSeq;
        final List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
        final Set<String> sequenceNames = new HashSet<String>();
        for (int numSequences = 0; numSequences < NUM_SEQUENCES && (refSeq = refSeqFile.nextSequence()) != null; ++numSequences) {
            if (sequenceNames.contains(refSeq.getName())) {
                throw new PicardException("Sequence name appears more than once in reference: " + refSeq.getName());
            }
            sequenceNames.add(refSeq.getName());
            ret.add(makeSequenceRecord(refSeq));
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        final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(INPUT, TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE);
        final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);

        ReferenceSequence seq = null;
        while ((seq = ref.nextSequence()) != null) {
            final String name  = seq.getName();
            final byte[] bases = seq.getBases();

            try {
                out.write(">");
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