# HG changeset patch
# User mzeidler
# Date 1380194628 14400
# Node ID be5d3889a1b927e851155c848720be4c00289a5e
# Parent  0d0b19f1b74073cf47c3536d98fdc90be7204ff5
Uploaded

diff -r 0d0b19f1b740 -r be5d3889a1b9 vmap.py
--- a/vmap.py	Thu Sep 26 07:10:09 2013 -0400
+++ b/vmap.py	Thu Sep 26 07:23:48 2013 -0400
@@ -1078,9 +1078,7 @@
                         '--outSAMattributes', 'Standard',
                         '--outSAMunmapped', 'Within',
                         '--outStd', 'SAM',
-                        '--outFilterMultimapNmax', '1000',
-                        '--outSAMprimaryFlag', 'AllBestScore',
-                        '--outSAMorder', 'PairedKeepInputOrder']
+                        '--outFilterMultimapNmax', '1000']
 
         if self.unmapped1 or self.unmapped2:
             star_cline += ['--outReadsUnmapped', 'Fastx']