Package net.sf.samtools

Examples of net.sf.samtools.SAMRecord.clearAttributes()

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      // Using a static variable because contigs may overlap multiple regions and cause dupes
      chunk.setReadName(chunk.getReadName() + "_" + chunkIdx++);
      chunk.setAlignmentStart(actualPos + calcIndelOffset(startIdx, contig.getCigar()));
      chunk.setCigar(cigar);
      chunk.setReadString(bases);
      chunk.clearAttributes();
//      chunk.setAttribute("ZZ", contig.getCigarString());
     
      chunk.setAttribute("ZZ", contig.getReferenceName() + ":" + contig.getAlignmentStart() +
          ":" + contig.getCigarString());
     
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