use strict; 
my %SAM; 
$SAM{chr2LHet} = 1; 
$SAM{chr2RHet} = 1; 
$SAM{chr3LHet} = 1; 
$SAM{chr3RHet} = 1; 
foreach my $chr (sort cmpChrs keys %SAM) { 
    print "CHR=$chr\n"; 
} 
sub cmpChrs () { 
    if($a =~ /chr(\d+)/) { 
        my $numa = $1; 
        if($b =~ /chr(\d+)/) { 
            my $numb = $1; 
            if($numa < $numb) { return 1; } 
            else { 
                $a =~ s/chr\d+//; 
                $b =~ s/chr\d+//; 
                my %temp; 
                $temp{$a}=1; 
                $temp{$b}=1; 
                foreach my $key (sort cmpChrs keys %temp) { 
                    if($key eq $a) { return 1; } 
                    else { return -1; } 
                } 
            } 
        } else { return 1; } 
    } 
    return 1; 
}

use strict; 
my %SAM; 
$SAM{chr2LHet} = 1; 
$SAM{chr2RHet} = 1; 
$SAM{chr3LHet} = 1; 
$SAM{chr3RHet} = 1; 
foreach my $chr (sort {cmpChrs($a,$b)} keys %SAM) { 
    print "CHR=$chr\n"; 
} 
sub cmpChrs () { 
    if($a =~ /chr(\d+)/) { 
        my $numa = $1; 
        if($b =~ /chr(\d+)/) { 
            my $numb = $1; 
            if($numa < $numb) { return 1; } 
            else { 
                $a =~ s/chr\d+//; 
                $b =~ s/chr\d+//; 
                my %temp; 
                $temp{$a}=1; 
                $temp{$b}=1; 
                foreach my $key (sort {cmpChrs($a,$b)} keys %temp) { 
                    if($key eq $a) { return 1; } 
                    else { return -1; } 
                } 
            } 
        } else { return 1; } 
    } 
    return 1; 
}

#!/usr/local/bin/perl 
 
use warnings; 
use strict; 
use 5.10.0; 
 
my %SAM; 
$SAM{chr12RHet} = 1; 
$SAM{chr13LHet} = 1; 
$SAM{chr2LHet} = 1; 
$SAM{chr2RHet} = 1; 
$SAM{chr3LHet} = 1; 
$SAM{chr3RHet} = 1; 
 
for my $chr ( sort { cmpChrs($a, $b) } keys %SAM ) { 
    say $1 if $chr =~ /chr\d+(.+)/; 
} 
 
 
sub cmpChrs { 
    ($a =~ /(\d+)/)[0] <=> ($b =~ /(\d+)/)[0]; 
}

for my $chr ( sort { ($a =~ /(\d+)/)[0] <=> ($b =~ /(\d+)/)[0] } keys %SAM ) { 
    say $1 if $chr =~ /chr\d+(.+)/; 
}

.... 
.... 
               # inefficiently sort by descending numeric compare using 
               # the first integer after the first = sign, or the 
               # whole record case-insensitively otherwise 
 
               @new = sort { 
                   ($b =~ /=(\d+)/)[0] <=> ($a =~ /=(\d+)/)[0] 
                                       || 
                               uc($a)  cmp  uc($b) 
               } @old; 
 
               # same thing, but much more efficiently; 
               # we'll build auxiliary indices instead 
               # for speed 
               @nums = @caps = (); 
               for (@old) { 
                   push @nums, /=(\d+)/; 
                   push @caps, uc($_); 
               } 
 
               @new = @old[ sort { 
                                   $nums[$b] <=> $nums[$a] 
                                            || 
                                   $caps[$a] cmp $caps[$b] 
                                  } 0..$#old 
                          ]; 
 
               # same thing, but without any temps 
               @new = map { $_->[0] } 
                      sort { $b->[1] <=> $a->[1] 
                                      || 
                             $a->[2] cmp $b->[2] 
                      } map { [$_, /=(\d+)/, uc($_)] } @old; 
.... 
....

D:\perl>char_boy.pl 
Can't undef active subroutine at D:\perl\char_boy.pl line 34 (#1) 
    (F) You can't undefine a routine that's currently running.  You can, 
    however, redefine it while it's running, and you can even undef the 
    redefined subroutine while the old routine is running.  Go figure. 
 
Uncaught exception from user code: 
        Can't undef active subroutine at D:\perl\char_boy.pl line 34. 
 at D:\perl\char_boy.pl line 34 
        main::cmpChrs called at D:\perl\char_boy.pl line 12 
Attempt to free unreferenced scalar: SV 0x1a39c0, Perl interpreter: 0x15da508 at C:/Perl64/lib/Carp.pm line 45. 
Attempt to free unreferenced scalar: SV 0x1a39c0, Perl interpreter: 0x15da508 at D:\perl\char_boy.pl line 34.