Package net.sf.cram

Examples of net.sf.cram.Cram2BamRecordFactory


    normalizer.normalize(cramRecords, true, refs, container.alignmentStart,
        container.h.substitutionMatrix, container.h.AP_seriesDelta);
    long time2 = System.nanoTime();

    Cram2BamRecordFactory c2sFactory = new Cram2BamRecordFactory(
        cramHeader.samFileHeader);

    long c2sTime = 0;

    for (CramRecord r : cramRecords) {
      long time = System.nanoTime();
      SAMRecord s = c2sFactory.create(r);
      c2sTime += System.nanoTime() - time;
      if (!r.segmentUnmapped)
        Utils.calculateMdAndNmTags(s, refs, restoreMDTag, restoreNMTag);

      s.setValidationStringency(validationStringency);
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Related Classes of net.sf.cram.Cram2BamRecordFactory

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