I doubt it will speed things up much, but looking through a hash is generally quicker than looking through an array. Change @IDS to %IDS, then you don't need the grep. 
$IDS{$id}++;
...
if ($A+$B == 2 && (exists $IDS{$TI})){

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In reply to Re: Script far too slow with large files - wisdom needed! by toolic
in thread Script far too slow with large files - wisdom needed! by biologistatsea

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