#!/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 = ();
        if (!eof(F1)) {
                (@in1) = split /\t/, <F1>;
                chomp $in1[2];
        }
}

sub getrec2 {
        @in2 = ();
        if (!eof(F2)) {
                (@in2) = split /\t/, <F2>;
                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 if $#in1<0;
                write1 if $#in2<0;
        }
        elsif ($in1[2] eq $in2[1]) {
                # Matching records, merge & write 'em
                writeboth;
        }
        elsif ($in1[2] lt $in2[1]) {
                # unmatched item in file 1, write it & get next rec
                write1;
        }
        else {
                # unmatched item in file 2, write it & get next rec
                write2;
        }
}