def sampe(args, opts):
    """
    %prog sampe database.fasta read1.fq read2.fq

    Wrapper for `bwa sampe`. Output will be read1.sam.
    """
    dbfile, read1file, read2file = args
    dbfile = check_index(dbfile)
    sai1file = check_aln(dbfile, read1file, cpus=opts.cpus)
    sai2file = check_aln(dbfile, read2file, cpus=opts.cpus)

    samfile, _, unmapped = get_samfile(read1file, dbfile,
                                       bam=opts.bam, unmapped=opts.unmapped)
    if not need_update((dbfile, sai1file, sai2file), samfile):
        logging.error("`{0}` exists. `bwa samse` already run.".format(samfile))
        return "", samfile

    cmd = "bwa sampe " + " ".join((dbfile, sai1file, sai2file,
                                   read1file, read2file))
    cmd += " " + opts.extra
    if opts.cutoff:
        cmd += " -a {0}".format(opts.cutoff)
    if opts.uniq:
        cmd += " -n 1"

    return cmd, samfile
def sampe ( args , opts ) : dbfile , read1file , read2file = args dbfile = check_index ( dbfile ) sai1file = check_aln ( dbfile , read1file , cpus = opts . cpus ) sai2file = check_aln ( dbfile , read2file , cpus = opts . cpus ) samfile , _ , unmapped = get_samfile ( read1file , dbfile , bam = opts . bam , unmapped = opts . unmapped ) if not need_update ( ( dbfile , sai1file , sai2file ) , samfile ) : logging . error ( "`{0}` exists. `bwa samse` already run." . format ( samfile ) ) return "" , samfile cmd = "bwa sampe " + " " . join ( ( dbfile , sai1file , sai2file , read1file , read2file ) ) cmd += " " + opts . extra if opts . cutoff : cmd += " -a {0}" . format ( opts . cutoff ) if opts . uniq : cmd += " -n 1" return cmd , samfile
%prog sampe database.fasta read1.fq read2.fq

    Wrapper for `bwa sampe`. Output will be read1.sam.