From c7553fce75b0ec81ee1ac597759482a4142a51a5 Mon Sep 17 00:00:00 2001
From: Carla Cummins <cc21@sanger.ac.uk>
Date: Tue, 20 Aug 2013 16:16:47 +0100
Subject: [PATCH] Bug fix in file existance check

Former-commit-id: 6e940ed33cbd4d7f88d74f056af201e745aa8894
---
 lib/Bio/Tradis/CommandLine/TradisAnalysis.pm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm b/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
index 3edf3a5..cff0be0 100644
--- a/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
+++ b/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
@@ -74,7 +74,8 @@ sub run {
 	my $fq = $self->fastqfile;
     open( FILES, "<", $fq );
     my @filelist = <FILES>;
-    my $file_dir = $self->get_file_dir;
+	my $file_dir = "";
+	unless($fq =~ /^\//){$file_dir = $self->get_file_dir;}
 	#check files exist before running
 	my $line_no = 0;
 	foreach my $f1 (@filelist){