my $newref = [
    map  { $_->[0] }
    sort { $a->[1] <=> $b->[1] || $a->[2] cmp $b->[2] }
    map  { my $s = $_->seq_region_name;
           [ $_, $s =~ m/^[0-9]+$/ ? $s : 999, lc $s ]
           }
    @$oldref ];
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