You're right. I overlooked the statement label in one of your next statements. I could not have arrived at my misreading if I had been as aware as you are that there are only two dozen chromosomes.

But what about your hash of arrays? Why would getting the data out be such a nightmare?

Populating the hash of arrays:

open my $annotation_read_handle, '<', $annotation_file;
my %annotations_for;
while (my $ad = <$annotation_read_handle> ) {
    # read $an_chrom out of $ad
    my ($an_chrom, undef) = split(/\t/, $ad);
    
    # store for future lookups
    push @$annotations_for{$an_chrom}, $ad;
}
close $annotation_read_handle;
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Now read through the main data file and assign each chromosome number to my $main_chrom.

    # look up the list of annotations relevant to the current chromoso
+me
    my $annotations_ref = $annotations_for{$main_chrom};
    # loop through just these annotations
    ILC: foreach my $ad (@$annotations_ref) { # ...
    }
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Of course—as other more enlightened commentators have already pointed out—the most important thing to optimize is the range_find subroutine.