From 0c73c8b3805448db36196aff0b800972b85863a7 Mon Sep 17 00:00:00 2001
From: chienchi <chienchi@lanl.gov>
Date: Tue, 22 Sep 2015 15:51:00 -0600
Subject: [PATCH] fix gap coordinate bug

---
 lib/PhaME.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/PhaME.pm b/lib/PhaME.pm
index 750e2bc..24bdc41 100644
--- a/lib/PhaME.pm
+++ b/lib/PhaME.pm
@@ -338,7 +338,7 @@ foreach my $begin (sort{$a<=>$b} keys %CDS){
    $last=$end;
 }
    if ($last < $source_end){
-      $gap_start = $end+1;
+      $gap_start = $last+1;
       print OUT "$name\t$gap_start\t$source_end\tnoncoding\n";
    }
 }