That was the first thing I though of also, although I would write it like this:

$found{$1}++ while /($foo|$bar|$baz)/go;
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The only problem in general is that $foo and company cannot contain any "special" regular expression character...it will work, but they will return the match, not the original search, i.e. $foo = "ba.t" would create keys of "bart", "bast", and "bait". Still, if you know your input file well enough to avoid them, a simple hash increment is definitely a smooth way to do it.