Mercurial > repos > yufei-luo > bwa_0_7_5
comparison bwa_0_7_5/bwa_0_7_5.py @ 3:8409cff2d740 draft
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 |