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mergefile.1

15    20    foo
22    30    bar
30    33    baz
14    22    fubar

mergefile.2

alpha    baz    17.30
gamma    foobar    22.35
gamma    bar    19.01
delta    fromish    33.03
sigma    bear    14.56

mergefile.out
bar     22      30      gamma   19.01
...
foobar  null    null    gamma   22.35
fromish null    null    delta   33.03
fubar   14      22      null    null

#!/usr/bin/perl -w
use strict;
use warnings;

open F1, 'sort -k3 mergefile.1|' or die "opening file 1";
open F2, 'sort -k2 mergefile.2|' or die "opening file 2";

open OUF, '>', 'mergefile.out' or die "opening output file";

my @in1;
my @in2;

sub getrec1 {
        @in1 = ();
...
                chomp $in1[2];
        }
}

sub getrec2 {
        @in2 = ();
...
                chomp $in2[2];
        }
}

sub write1 {
        print OUF "$in1[2]\t$in1[0]\t$in1[1]\tnull\tnull\n";
        getrec1;
}

sub write2 {
        print OUF "$in2[1]\tnull\tnull\t$in2[0]\t$in2[2]\n";
        getrec2;
}

sub writeboth {
        print OUF "$in1[2]\t$in1[0]\t$in1[1]\t$in2[0]\t$in2[2]\n";
        getrec1;
        getrec2;
}

# Prime the pump
getrec1;
getrec2;

while (1) {
        last if $#in1<0 and $#in2<0;

        if ($#in1<0 or $#in2<0) {
                # Only one file is left...
...
                write2;
        }
}

bar    null    null    gamma    19.01
bar    22    30    null    null
...
foobar    null    null    gamma    22.35
fromish    null    null    delta    33.03
fubar    14    22    null    null

I altered the line "chomp $in2[2];" to read "chomp $in2[1];"