Re: Faulty Control Structures?

[Errto]

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.

[bioinformatics]

Mmmm... The data won't match up your right. I can adjust the window values and chromosome numbers to match up so that you do get output however. I just threw up data to illustrate.