Error when passing the "--mode" option of gsnap via "--extra-args"

[jnktsj]

When I ran MethylCoder with gsnap by passing arguments like: --extra-args "--mode=cmet-stranded -Q -n 1 -t 4"

KeyError: 'cmet' was raised.

I think cmet variable in gsnap.py should be declared beforehand so that we can avoid the error when the --mode argument is specified in the --extra-args.

def run_gsnap(gsnap_dir, gsnap_args, out_dir, ref_fasta, reads_paths, cpu_count):
    ref_base = op.splitext(ref_fasta)[0]
    ref_name = op.basename(ref_base)
    ref_dir = op.dirname(ref_fasta)
    reads_paths = [op.abspath(r) for r in reads_paths]
    log = op.join(out_dir, "gsnap_run.log")

    # cmet = " "  <--- declare beforehand
    if not "--mode" in gsnap_args:
        cmet = "--mode=cmet-nonstranded"
        print >>sys.stderr, "using non-stranded mode, specify " \
         + " --mode=cmet-stranded in --extra-args for stranded mode"

    if any(r.endswith(".gz") for r in reads_paths):
        gsnap_args += " --gunzip "

    reads_paths_str = " ".join(reads_paths)
    out_sam = op.abspath(op.join(out_dir, "methylcoded.gsnap.sam"))
    cmd = "gsnap --quiet-if-excessive -A sam -k 15 "
    cmd += " --nofails --nthreads %(cpu_count)i -D %(ref_dir)s %(gsnap_args)s"

    # KeyError: 'cmet' occurs because cmet cannot be generated when the "--mode" string is in gsnap_args
    cmd += " -d %(ref_name)s %(cmet)s %(reads_paths_str)s > %(out_sam)s 2> %(log)s"
    cmd %= locals()