BTW this bit of code doesn't do what you think it does

        push @{ $hash_of_chroms{$chr} }, $coord
          unless defined $hash_of_chroms{$chr}[$coord];   # don't add 
+duplicates
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push adds the item to the end of the list and you check some list element off in the far distance.

i.e. if the array is empty and $coord = 50, then your code does this:-

     $array[0] = $coord unless $array[50];
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