in reply to Faulty Control Structures?

I tried running the program on the data you provided but it exited instantly and printed no output in output.txt so I assume that data is not representative. I don't exactly understand what the code is doing but I don't see anything that could cause an infinite loop. I see two things that make me suspicious: 1) your range data is all numbers but you're using the character-operators lt and eq to compare them, and 2) these lines:

# look to see if the windows don't overlap if ($test lt $window[0]) {return 0;} # look to see if the windows don't overlap elsif ($test2 lt $probe[0]) {return 0;}
are inside a loop in which the iterator variable is $value1, yet they don't consider that value.

Update: Second thought - the second part of the code seems, if I understand it, to be designed to take two ranges of numbers and see if they overlap. To do so, it actually expands the ranges into lists and compares them one-by-one. This becomes, in the worst case, an N^2 calculation for what should be a constant operation:

sub range_overlap { my ($start1, $end1, $start2, $end2); return ($end1 >= $start2 || $start1 <= $end2) && ($end2 >= $start1 || $start2 <= $end1); }
untested but it should be about right.