From 94e2961e30c7df7773eba19189e594620dff26d9 Mon Sep 17 00:00:00 2001
From: Lance Parsons <lparsons@princeton.edu>
Date: Thu, 4 Sep 2014 16:02:54 -0400
Subject: [PATCH] Allow specification of complete filename of 2bit files in
 codingSnps.pl

---
 tools/evolution/codingSnps.pl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tools/evolution/codingSnps.pl b/tools/evolution/codingSnps.pl
index 941ff73c7d0..0edb22f2038 100755
--- a/tools/evolution/codingSnps.pl
+++ b/tools/evolution/codingSnps.pl
@@ -564,6 +564,8 @@ sub getGalaxyInfo {
    if ($nibDir eq 'Galaxy') {
       print STDERR "Failed to find sequence directory in locfile $locFile\n";
    }
-   $nibDir .= "/$build.2bit";  #we want full path and filename
+   # lparsons: allow specification of full filename in loc file for greater felxibility
+   unless ($nibDir =~ /(.*)\.2bit/) { $nibDir .= "/$build.2bit"; }
+   #$nibDir .= "/$build.2bit";  #we want full path and filename
 }