code: def samse(args, opts):
      
      dbfile, readfile = args
      dbfile = check_index(dbfile)
      saifile = check_aln(dbfile, readfile, cpus=opts.cpus)
  
      samfile, _, unmapped = get_samfile(readfile, dbfile,
                                         bam=opts.bam, unmapped=opts.unmapped)
      if not need_update((dbfile, saifile), samfile):
          logging.error("`{0}` exists. `bwa samse` already run.".format(samfile))
          return "", samfile
  
      cmd = "bwa samse {0} {1} {2}".format(dbfile, saifile, readfile)
      cmd += " " + opts.extra
      if opts.uniq:
          cmd += " -n 1"
  
      return cmd, samfile
docs: %prog samse database.fasta short_read.fastq
  
      Wrapper for `bwa samse`. Output will be short_read.sam.