/** * query containing - get reads contained by the specified interval * * @param contig the contig index string * @param start the start position * @param stop the stop position */ public void queryContained( String contig, int start, int stop ) { this.overlapping = false; initialize(contig, start, stop); }
/** * query containing - get reads contained by the specified interval * * @param contig the contig index string * @param start the start position * @param stop the stop position */ public void queryOverlapping( String contig, int start, int stop ) { this.overlapping = true; initialize(contig, start, stop); }