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#! /usr/bin/perl -w

use strict;
use warnings;

# fastq_paired_reads_convention2.pl [input file] [left output file] [right output file]

die "Check arguments" unless @ARGV == 3;

#open (LEFT, '>data/left2.fastq') or die "Cannot create $ARGV[1]: $!\n";
#open (RIGHT, '>data/right2.fastq') or die "Cannot create $ARGV[2]: $!\n";
#open (INPUT, '<data/interlaced.fastq') or die "Cannot open $ARGV[0]: $!\n";

open (LEFT, '>', $ARGV[1]) or die "Cannot create $ARGV[1]: $!\n";
open (RIGHT, '>', $ARGV[2]) or die "Cannot create $ARGV[2]: $!\n";
open (INPUT, '<', $ARGV[0]) or die "Cannot open $ARGV[0]: $!\n";

my $which = 0;
my $current_id;

while(<INPUT>) {
	chomp;
	if(/ 1\S*/){
		$_ =~ s/ 1\S*//;
		$_.='/1';
		$current_id = substr $_, 1;
		$which = 1;
	}
	if(/ 2\S*/){
		$_ =~ s/ 2\S*//;
		$_.='/2';
		$current_id = substr $_, 1;
		$which = 2;
	}
	
	if($_ eq '+'){
		$_.=$current_id;
	}
	
	if($which == 1){
		print LEFT "$_\n";
	}
	if($which == 2){
		print RIGHT "$_\n";
	}
}

close (LEFT);
close (RIGHT);
close (INPUT);