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comparison bwa_0_7_5/bwa_0_7_5.py @ 3:8409cff2d740 draft

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corrected the bug
author yufei-luo
date Fri, 29 Nov 2013 04:59:38 -0500
parents 839e36b39c3f
children 22449c3a0b7f
comparison
equal deleted inserted replaced
2:2c7b77f5919f 3:8409cff2d740
223 223
224 224
225 if args.genAlignType == 'paired': 225 if args.genAlignType == 'paired':
226 cmd = 'bwa mem %s %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, rfastq, end_cmds, args.output ) 226 cmd = 'bwa mem %s %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, rfastq, end_cmds, args.output )
227 else: 227 else:
228 cmd = 'bwa mem %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, end_cmds, args.output ) 228 cmd = 'bwa mem %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, end_cmds, args.output )
229 229
230 # perform alignments 230 # perform alignments
231 buffsize = 1048576 231 buffsize = 1048576
232 try: 232 try:
233 # need to nest try-except in try-finally to handle 2.4 233 # need to nest try-except in try-finally to handle 2.4