Mercurial > repos > mzeidler > virana_main

diff vmap.py @ 9:be5d3889a1b9 draft

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Uploaded
author mzeidler
date Thu, 26 Sep 2013 07:23:48 -0400
parents f63d639b223c
children
line wrap: on
line diff
--- 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']