def get_bamprep(x, config): params = bamprep._get_prep_params({"config": {"algorithm": config.get("algorithm", {})}}) if params["realign"] == "gatk" and params["recal"] == "gatk": return "gatk" elif not params["realign"] and not params["recal"]: return "none" else: raise ValueError("Unexpected bamprep approach: %s" % params)
def get_bamprep(x, config): params = bamprep._get_prep_params({"config": {"algorithm": config["algorithm"]}}) if params["realign"] == "gatk" and params["recal"] == "gatk": return "gatk" elif not params["realign"] and not params["recal"]: return "none" else: raise ValueError("Unexpected bamprep approach: %s" % params)
def get_bamprep(x, config): params = bamprep._get_prep_params({"config": {"algorithm": config.get("algorithm", {})}}) if params["realign"] == "gatk" and params["recal"] == "gatk": return "gatk" elif not params["realign"] and not params["recal"]: return "none" elif not params.get("recal") or not params.get("realign"): return "mixed" else: return ""