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Anonymous committed 16b1b8b

fixed bug to prevent BWA output from being malformed after AWS eviction

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Files changed (1)

tools/sr_mapping/bwa_wrapper.py

     except:
         sys.stdout.write( 'Could not determine BWA version\n' )
 
+    # check that output file is empty
+    if os.path.exists(options.output):
+        os.remove(options.output)
+
     # check for color space fastq that's not double-encoded and exit if appropriate
     if options.color_space:
         if not check_is_double_encoded( options.fastq ):