Hello james28909,

First, the code snippet provided is incomplete, and contains at least one, and probably two, syntax errors. Second, to understand what you are trying to do, I think we will need to see sample input data, together with the desired output. In the meantime I will make one observation: this line:

if ($md50 !~ $md51 && $filename0 =~ $filename1){
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is unlikely to work correctly across all cases. For example, if $md50 is '123456' and $md51 is '12345', the first condition will evaluate to false (because the match succeeds); but (I’m guessing) the logic of your code requires it to be true. Much simpler to use ne and eq here in place of !~ and =~, respectively:

if ($md50 ne $md51 && $filename0 eq $filename1){
[download]

Hope that helps,