Package net.sf.cram

Examples of net.sf.cram.Cram2BamRecordFactory.create()

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    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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