Retrieve snpEff arguments supplied through input configuration.

def _snpeff_args_from_config(data):
    """Retrieve snpEff arguments supplied through input configuration.
    """
    config = data["config"]
    args = ["-hgvs"]
    # General supplied arguments
    resources = config_utils.get_resources("snpeff", config)
    if resources.get("options"):
        args += [str(x) for x in resources.get("options", [])]
    # cancer specific calling arguments
    if vcfutils.get_paired_phenotype(data):
        args += ["-cancer"]

    effects_transcripts = dd.get_effects_transcripts(data)
    if effects_transcripts in set(["canonical_cancer"]):
        _, snpeff_base_dir = get_db(data)
        canon_list_file = os.path.join(snpeff_base_dir, "transcripts", "%s.txt" % effects_transcripts)
        if not utils.file_exists(canon_list_file):
            raise ValueError("Cannot find expected file for effects_transcripts: %s" % canon_list_file)
        args += ["-canonList", canon_list_file]
    elif effects_transcripts == "canonical" or tz.get_in(("config", "algorithm", "clinical_reporting"), data):
        args += ["-canon"]
    return args