Examples of net.sf.samtools.SAMFileReader.queryUnmapped()

    }
    threads.waitForAllThreadsToComplete();
    
    // Now go back and retrieve the unmapped reads.
    System.err.println("Processing unmapped reads");
    Iterator<SAMRecord> iter = rdr.queryUnmapped();
    while (iter.hasNext()) {
      SAMRecord read = iter.next();
    
      // If this read is not assigned a position, but the mate is, include in the output BAM associated with mate's chromosome.
      if (read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && read.getMateReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {

    SAMRecordIterator it1, it2;
    if (params.location != null) {
      AlignmentSliceQuery query = new AlignmentSliceQuery(params.location);
      if (SAMRecord.NO_ALIGNMENT_REFERENCE_NAME.equals(query.sequence)) {
        it1 = r1.queryUnmapped();
        it2 = r2.queryUnmapped();
      } else {
        it1 = r1.queryContained(query.sequence, query.start, query.end);
        it2 = r2.queryContained(query.sequence, query.start, query.end);
      }
    } else {

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