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#!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
my $curr_dir = cwd();
foreach my $file (<*_R1*.fastq*>, <*_R1*.fq*>, <*.R1*.fastq*>, <*.R1*.fq*>) {
$file =~ /^(\S+)[\._]R1[\._].*f(ast)?q/ or die "Error, cannot decipher filename $file";
my $core = $1;
my $right_fq = $file;
$right_fq =~ s/([\._])R1([\._])/$1R2$2/ or die "Error, cannot convert R1 to R2 in $right_fq";
unless (-s $right_fq) {
die "Error, cannot find Right.fq file corresponding to $file";
}
print join("\t", $core, "$curr_dir/$file", "$curr_dir/$right_fq") . "\n";
}
exit(0);
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