Ejemplos de _get_prep_params en Python

Ejemplo n.º 1

Archivo: validateplot.py Proyecto: TotallyBullshit/bcbio-nextgen

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)

Ejemplo n.º 2

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)

Ejemplo n.º 3

Archivo: validateplot.py Proyecto: hlkfoz/bcbio-nextgen

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 ""

Ejemplo n.º 4

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 ""