Package htsjdk.samtools.reference

Examples of htsjdk.samtools.reference.ReferenceSequence

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        // Design the baits!
        int discardedBaits = 0;
        final IntervalList baits = new IntervalList(targets.getHeader());
        for (final Interval target : targets) {
            final int sequenceIndex = targets.getHeader().getSequenceIndex(target.getSequence());
            final ReferenceSequence reference = referenceWalker.get(sequenceIndex);

            for (final Bait bait : DESIGN_STRATEGY.design(this, target, reference)) {
                if (bait.length() != BAIT_SIZE) {
                    throw new PicardException("Bait designed at wrong length: " + bait);
                }
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     * @return SAMSequenceRecords containing info from the fasta, plus from cmd-line arguments.
     */
    SAMSequenceDictionary makeSequenceDictionary(final File referenceFile) {
        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));
        }
        return new SAMSequenceDictionary(ret);
    }
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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(">");
                out.write(name);
                out.newLine();
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        if (refFile != null) {
            intervalToGc = new HashMap<Interval,Double>();
            for (final Interval target : uniqueTargets) {
                final ReferenceSequence rs = refFile.getSubsequenceAt(target.getSequence(), target.getStart(), target.getEnd());
                intervalToGc.put(target,SequenceUtil.calculateGc(rs.getBases()));
            }
        }

        setup(accumulationLevels, samRgRecords);
    }
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    public void acceptRecord(final SAMRecordAndReference args) {
      mappedRecordCount++;

      final SAMRecord samRecord = args.getSamRecord();
      final ReferenceSequence referenceSequence = args.getReferenceSequence();

      final byte[] readBases = samRecord.getReadBases();
      final byte[] readQualities = samRecord.getBaseQualities();
      final byte[] refBases = referenceSequence.getBases();

      if (samRecord.getReadLength() < minReadLength) {
        smallReadCount++;
        return;
      } else if (SequenceUtil.countMismatches(samRecord, refBases, true) > Math.round(samRecord.getReadLength() * maxMismatchRate)) {
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            }

            @Override
            public ReferenceSequence getSequence(final String contig) {
                if (contig.equals(record.getSequenceName())) {
                    return new ReferenceSequence(record.getSequenceName(), 0, referenceString.getBytes());
                } else {
                    return null;
                }
            }
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Related Classes of htsjdk.samtools.reference.ReferenceSequence

  • org.broadinstitute.gatk.engine.alignment.reference.bwt.CreateBWTFromReference
  • org.broadinstitute.gatk.engine.alignment.reference.packing.CreatePACFromReference
  • org.broadinstitute.gatk.engine.datasources.providers.LocusReferenceViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceView
  • org.broadinstitute.gatk.tools.walkers.qc.QCRef
  • org.broadinstitute.gatk.tools.walkers.readutils.ClipReads
  • org.broadinstitute.gatk.utils.baq.BAQ
  • org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile
  • org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFileUnitTest
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