# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1389994243 18000
# Node ID ab4c4e07eb3c94b9aa41d228bbf416cdd510d690
# Parent  05ca4081ca7e74dd582b11dd5a013ac01f63abd6
Fix for using built-in reference data.

diff -r 05ca4081ca7e -r ab4c4e07eb3c sam_to_bam.py
--- a/sam_to_bam.py	Thu Jan 09 14:29:01 2014 -0500
+++ b/sam_to_bam.py	Fri Jan 17 16:30:43 2014 -0500
@@ -48,7 +48,6 @@
         # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
         # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
         # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
-        fai_index_file_base = seq_path
         fai_index_file_path = '%s.fai' % options.index
         if not os.path.exists( fai_index_file_path ):
             #clean up temp files