The Schwartzian transform is the classic way to do this. First transform your multi-dimensional array to a list of key/reference pairs where the key is some hash of the values you want to sort on (a unique hash is best :) and the reference is a reference to the row the key pertains to. Then sort the pairs by the key. Finally pull the rows out and you're done.

use strict;
use warnings;

my @chrnums = (
    [qw(chr1 10)],
    [qw(chr3 20)],
    [qw(chr1 30)],
    [qw(chr3 5)],  
    [qw(chr5 5)],
    );

@chrnums = map {
    #Extract sorted rows
    $_->[1]
    } sort {$a->[0] cmp $b->[0]} map {
    #Transform to keys and refs
    [(sprintf "%5d%5d", $_->[0] =~ /(\d+)/, $_->[1]), $_]
    } @chrnums;

print "$_->[0] $_->[1]\n" for @chrnums;
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Prints:

chr1 10
chr1 30
chr3 5
chr3 20
chr5 5
[download]