# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1382453072 18000
# Node ID 8fac6c7d32fdb95a33ce7abbd01630948e8ea5d7
# Parent  8180f6b0249b458b5a4bb891a0f8473b559013c2
Copy reference fasta for shear sv to avoid GATK issue with symlinks

diff -r 8180f6b0249b -r 8fac6c7d32fd shear_wrapper.py
--- a/shear_wrapper.py	Tue Oct 22 08:20:52 2013 -0500
+++ b/shear_wrapper.py	Tue Oct 22 09:44:32 2013 -0500
@@ -47,7 +47,7 @@
     args.append( command )
     # Check required params for command
     buffsize = 1048576 
-    copy_ref = False
+    copy_ref = True
     prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref'
     if command in ['sv']:
         args.append( '-p' )
@@ -57,6 +57,7 @@
         if options.region:
             args.append('-r')
             args.append(options.region)
+        copy_ref = True # GATK has issue with symlinks for .fa and .fai 
     if options.svidx_dir and command in ['sv']:
         if not os.path.isdir(options.svidx_dir):
             os.makedirs(options.svidx_dir)