code: function isAlignmentInRange(read: SamRead,
                              idxRange: ContigInterval<number>,
                              contained: boolean): boolean {
    // TODO: Use cigar.getReferenceLength() instead of l_seq, like htsjdk. 
    var readRange = new ContigInterval(read.refID, read.pos, read.pos + read.l_seq - 1);
    if (contained) {
      return idxRange.containsInterval(readRange);
    } else {
      return readRange.intersects(idxRange);
    }
  }
docs: The 'contained' parameter controls whether the alignments must be fully
  contained within the range, or need only overlap it.