#!/usr/bin/perl -w

my $fq1 = $ARGV[0] or die "merge.fastq.pl. fastq1 fastq2 outfastq\n";
my $fq2 = $ARGV[1] or die "merge.fastq.pl. fastq1 fastq2 outfastq\n";
my $fq3 = $ARGV[2] or die "merge.fastq.pl. fastq1 fastq2 outfastq\n";
open (PE, $fq1) || &ErrorMessage($fq1);
open (PF, $fq2) || &ErrorMessage($fq2);
open (PH, ">$fq3") || &ErrorMessage($fq3);
while(<PE>) {
        print PH $_;
}
close PE;
while(<PF>) {
        print PH $_;
}
close PF;
close PH;
sub ErrorMessage {
        my $err = shift;
        return "Fatal error: $err does not exist\n";
        exit(1);        
}