code: public static <T extends Locatable> void setTraversalParameters(Configuration conf,
  			List<T> intervals, boolean traverseUnplacedUnmapped) {
  		if (intervals == null && !traverseUnplacedUnmapped) {
  			throw new IllegalArgumentException("Traversing mapped reads only is not supported.");
  		}
  		conf.setBoolean(BOUNDED_TRAVERSAL_PROPERTY, true);
  		if (intervals != null) {
  			StringBuilder sb = new StringBuilder();
  			for (Iterator<T> it = intervals.iterator(); it.hasNext(); ) {
  				Locatable l = it.next();
  				sb.append(String.format("%s:%d-%d", l.getContig(), l.getStart(), l.getEnd()));
  				if (it.hasNext()) {
  					sb.append(",");
  				}
  			}
  			conf.set(INTERVALS_PROPERTY, sb.toString());
  		}
  		conf.setBoolean(TRAVERSE_UNPLACED_UNMAPPED_PROPERTY, traverseUnplacedUnmapped);
  	}
docs: Only include reads that overlap the given intervals (if specified) and unplaced
  unmapped reads (if <code>true</code>).
  @param conf the Hadoop configuration to set properties on
  @param intervals the intervals to filter by, or <code>null</code> if all reads
  are to be included (in which case <code>traverseUnplacedUnmapped</code> must be
  <code>true</code>)
  @param traverseUnplacedUnmapped whether to included unplaced unampped reads
  @param <T> the {@link Locatable} type