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;
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) { # ...
}
Of course—as other more enlightened commentators have already pointed out—the most important thing to optimize is the range_find subroutine.
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