Mercurial > repos > geert-vandeweyer > mutect_wrapper
comparison mutect_wrapper.py @ 15:37a8219b62de draft
Fixes. MuTect now works
| author | geert-vandeweyer |
|---|---|
| date | Mon, 17 Feb 2014 11:53:56 -0500 |
| parents | 59c387dcb2d2 |
| children |
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| 14:e670ffb1c356 | 15:37a8219b62de |
|---|---|
| 86 | 86 |
| 87 # all parameters set? | 87 # all parameters set? |
| 88 #if options.params != 'pre_set': | 88 #if options.params != 'pre_set': |
| 89 | 89 |
| 90 # final command | 90 # final command |
| 91 command = 'java -Xmx2G -jar %s %s ' % (options.jar, arguments) | 91 command = 'java -Xmx2G -jar %s %s ' % (''.join(options.jar), arguments) |
| 92 #print command | 92 print command |
| 93 try: | 93 try: |
| 94 os.system(command) | 94 os.system(command) |
| 95 except: | 95 except: |
| 96 raise "muTect Failed" + str(e) | 96 raise "muTect Failed" + str(e) |
| 97 #if tmp_dir and os.path.exists( tmp_dir ): | 97 #if tmp_dir and os.path.exists( tmp_dir ): |