Your for loop syntax is broken. It should be:

    for my $Skmerkey (keys %Skmer) {

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In several places you use () instead of {} for accessing hash values. The code should look like:

        my $i = $Skmer{$Skmerkey};

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I strongly recommend you use strictures (use strict; use warnings; - see The strictures, according to Seuss). You initialize the array @array2 but access $arrayS2[...] in several places. Strictures would have found that for you immediately.

Your first while loop references <IN>, but nothing opens IN as a file handle.

\chomp($line) is incorrect. Remove the \.

Premature optimization is the root of all job security

In reply to Re: FInding the longest match from an initial match between two files by GrandFather
in thread FInding the longest match from an initial match between two files by Allie_grater

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