in reply to passing multiple hashes to a subroutine

Hashes and arrays are the same in array context. Try print join(", ", @_);at the beginning of your sub to see the effect.

I suggest passing references instead of hashes:

sub count_orientation { my $ref = shift; my $x = shift; my $y = shift; $x->{$ref}{amount}++; if ($y->{$ref}{orientation} eq "for"){ $x->{$ref}{amountFor}++; } else { $x->{$ref}{amountRev}++; } } &count_orientation ($ref_end, \%error_start, \%score);

Always remember that you're working on your original hashes when using references:

sub foo { my $hashref = shift; delete $hashref->{a}; print keys %$hashref; } %x = (a => 1, b => 2); foo(\%x); print $x{a};
The sub will modify the original %x and $x{a} is gone away at the last line.