def __init__(self, picard_ref, gatk_dir, config): resources = config_utils.get_resources("gatk", config) self._jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx2g"]) self._picard_ref = config_utils.expand_path(picard_ref) self._gatk_dir = config_utils.expand_path(gatk_dir) or config_utils.expand_path(picard_ref) self._config = config self._gatk_version, self._picard_version = None, None
def __init__(self, picard_ref, gatk_dir, config): resources = config_utils.get_resources("gatk", config) self._jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx2g"]) self._picard_ref = config_utils.expand_path(picard_ref) self._gatk_dir = config_utils.expand_path( gatk_dir) or config_utils.expand_path(picard_ref) self._config = config self._gatk_version, self._picard_version = None, None
def _find_snpeff_datadir(config_file): with open(config_file) as in_handle: for line in in_handle: if line.startswith("data_dir"): data_dir = config_utils.expand_path(line.split("=")[-1].strip()) if not data_dir.startswith("/"): data_dir = os.path.join(os.path.dirname(config_file), data_dir) return data_dir raise ValueError("Did not find data directory in snpEff config file: %s" % config_file)