Thanks for all the help guys - really appreciate it. I wanted to be able to add more options (-x, -y, -z) easily, and to do it I ended up using an array of hashes - @arrAllArgs. When I enter:

perl myScript -i origSamples,moreSamples -p 1,3 -o 100,200

There is now a separate statement for parsing each argument:

parseNumericArgList($args{p}, 'pipeline', 1);
parseNumericArgList($args{o}, 'overlap', 1);
[download]

And the subroutine (it's long winded but I can understand it):

sub parseNumericArgList {

    my ($arg, $tag, $deflt) = @_;

    my $sing = 0;
    my @new = ();
    if (defined($arg)) {
        # a list was entered
        if ($arg =~ /,/) {
            my @singles = split(",", $arg);
            foreach $sing (@singles) {
                if ($sing =~ /\D/) {
                    print "\n\nWrong value in $tag\n\n";
                    die $USAGE
                } else {
                    if (scalar(@arrAllArgs) == 0) {
                        push (@new, addToRef($allArgs, $tag, $sing));
                    } else {
                        foreach $allArgs (@arrAllArgs) {
                            push (@new, addToRef($allArgs, $tag, $sing
+));
                        }
                    }
                }
            }
        } else {
            # a single value was entered
            if ($arg =~ /\D/) {
                print "\n\nWrong value in $tag\n\n";
                die $USAGE
            }
            if (scalar(@arrAllArgs) == 0) {
                push (@new, addToRef($allArgs, $tag, $arg));
            } else {
                foreach $allArgs (@arrAllArgs) {
                    push (@new, addToRef($allArgs, $tag, $arg));
                }
            }
        }
    } else {
        # nothing was entered, use default
        if (scalar(@arrAllArgs) == 0) {
            push (@new, addToRef($allArgs, $tag, $deflt));
        } else {
            foreach $allArgs (@arrAllArgs) {
                push (@new, addToRef($allArgs, $tag, $deflt));
            }
        }
    }
    @arrAllArgs = ();
    @arrAllArgs = @new;
}

sub addToRef {

    my ( $refIn, $addNm, $addVal ) = @_;
    my $ref = {};
    
    my $k = "";
    foreach $k (keys %{$refIn}) {
    $ref->{$k} = $refIn->{$k};
    }
    $ref->{$addNm} = $addVal;
    return $ref;
}
[download]

This provides me with the array of hashes @arrAllArgs

0  HASH(0x9e2930)
   'overlap' => 100
   'pipeline' => 1
1  HASH(0x9e55f0)
   'overlap' => 200
   'pipeline' => 1
2  HASH(0x9e2910)
   'overlap' => 100
   'pipeline' => 3
3  HASH(0xd8ead0)
   'overlap' => 200
   'pipeline' => 3
[download]

And then when I get to the main block of code it's a simple matter of

foreach $run (@arrAllArgs) {
    foreach $ak (keys %{$run}) {
        $runArgs{$ak} = $run->{$ak};
    }
    processOne();
}
[download]

Have to add a bit to cope with non-numeric arguments and I'm there. Hope this helps anyone else in the same sitch....

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