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#!/usr/bin/perl
use strict;
use warnings;
# make sure delimiter is properly escaped, e.g. for "+" we need "\+".
my $delimiter = $ARGV[0];
my $infileA = $ARGV[1];
my $infileB = $ARGV[2];
my $rc2 = $ARGV[3];
open(INA, $infileA) or die "Can't read $infileA\n";
open(INB, $infileB) or die "Can't read $infileB\n";
my $fastaHeader = "";
#sub revcompl {
# return ((my $rev = reverse $_) =~ tr/ACGTacgt/TGCAtgca/);
#}
while(<INA>)
{
my $a = $_;
my $b = <INB>;
chomp $a;
chomp $b;
if($rc2)
{
# $b = revcompl($b);
$b = reverse $b;
$b =~ tr/ACGTacgt/TGCAtgca/;
}
print $a . $delimiter . $b . "\n";
}
close INA;
close INB;
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