#!/usr/bin/perl

###############################
# 
# ConFinder requires an input
# directory containing files
# with *.fastq or *.fq 
#
###############################

$fold=shift(@ARGV);

$dat = shift(@ARGV);
$fq = shift(@ARGV);
$fq=~s/\.gz//;

# If we're here the file should be some type
# of fastq data type, append .fq if it's 
# missing 
if(!(($fq=~/\.fastq$/)||($fq=~/\.fq$/))) {
  $fq=$fq.".fq";
}

`ln -s $dat $fold/$fq\n`;