def check_gaps(matches, gap_threshold = <NUM_LIT:0>):
gaps = []<EOL>prev = None<EOL>for match in sorted(matches, key = itemgetter(<NUM_LIT:0>)):<EOL><INDENT>if prev is None:<EOL><INDENT>prev = match<EOL>continue<EOL><DEDENT>if match[<NUM_LIT:0>] - prev[<NUM_LIT:1>] >= gap_threshold:<EOL><INDENT>gaps.append([prev, match])<EOL>prev = match<EOL><DEDENT><DEDENT>return [[i[<NUM_LIT:0>][<NUM_LIT:1>], i[<NUM_LIT:1>][<NUM_LIT:0>]] for i in gaps]<EOL>
check for large gaps between alignment windows