Retrieve snpEff base command line.

def _get_snpeff_cmd(cmd_name, datadir, data, out_file):
    """Retrieve snpEff base command line.
    """
    resources = config_utils.get_resources("snpeff", data["config"])
    jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx3g"])
    # scale by cores, defaulting to 2x base usage to ensure we have enough memory
    # for single core runs to use with human genomes.
    # Sets a maximum amount of memory to avoid core dumps exceeding 32Gb
    # We shouldn't need that much memory for snpEff, so avoid issues
    # https://www.elastic.co/guide/en/elasticsearch/guide/current/heap-sizing.html#compressed_oops
    jvm_opts = config_utils.adjust_opts(jvm_opts, {"algorithm": {"memory_adjust":
                                                                 {"direction": "increase",
                                                                  "maximum": "30000M",
                                                                  "magnitude": max(2, dd.get_cores(data))}}})
    memory = " ".join(jvm_opts)
    snpeff = config_utils.get_program("snpEff", data["config"])
    java_args = "-Djava.io.tmpdir=%s" % utils.safe_makedir(os.path.join(os.path.dirname(out_file), "tmp"))
    export = "unset JAVA_HOME && export PATH=%s:\"$PATH\" && " % (utils.get_java_binpath())
    cmd = "{export} {snpeff} {memory} {java_args} {cmd_name} -dataDir {datadir}"
    return cmd.format(**locals())