Package net.sf.picard.reference

Examples of net.sf.picard.reference.ReferenceSequence

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    ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(args[1]));
    SAMRecordIterator iterator = reader.iterator();
    String refName = iterator.next().getReferenceName();
    iterator.close();
    ReferenceSequence sequence = ref.getSequence(refName);

    iterator = reader.iterator();
    Sam2CramRecordFactory factory = new Sam2CramRecordFactory(sequence.getBases());
    factory.preserveReadNames = false;
    factory.captureAllTags = false;
    factory.captureUnmappedBases = true;
    factory.captureUnmappedScores = true;
    factory.preserveReadNames = true;
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    if (container.sequenceId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
      refs = new byte[] {};
    } else if (prevSeqId < 0 || prevSeqId != container.sequenceId) {
      SAMSequenceRecord sequence = cramHeader.samFileHeader
          .getSequence(container.sequenceId);
      ReferenceSequence referenceSequence = Utils
          .trySequenceNameVariants(referenceSequenceFile,
              sequence.getSequenceName());
      refs = referenceSequence.getBases();
      prevSeqId = container.sequenceId;
    }

    long time1 = System.nanoTime();
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Related Classes of net.sf.picard.reference.ReferenceSequence

  • net.sf.cram.Bam2Cram
  • net.sf.cram.BLOCK_PROTO
  • net.sf.cram.Cram2Bam
  • net.sf.cram.SpotAssemblyTest
  • net.sf.cram.Utils
  • net.sf.picard.sam.SamFileValidator
  • net.sf.samtools.SAMIterator
  • org.tgen.sol.SNP.SolSNP
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