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while ((my $begin, my $end) =  each %exon_endpoints) {
    print get_exon($chromosome, $begin, $end), "\n\n";
...
    # The arguments to substr are: string, beginning, length
    return substr($chromosome, $begin - 1, $end - $begin + 1);
}

while ((my $begin, my $end) =  each %exon_endpoints) {
    print substr($chromosome, $begin - 1, $end - $begin + 1), "\n\n";
}

my $chromosome;
get_chromosome(1, \$chromosome);
...
{
    print $get_exon->(@ends), "\n\n";
}