def __init__(self, jar="snpEff.jar", javatmp=os.getcwd(), max_memory=None):
if not jar:
raise IOError("Fail to load snpEff tools~")
self.jar = os.path.abspath(jar)
JavaTool.__init__(self,
self.jar,
tmp_path=os.path.abspath(javatmp),
max_memory=max_memory)
def __init__(self,
jar_path="",
javatmp=os.getcwd(),
max_memory=None,
**kwargs):
if not jar_path:
raise IOError("Fail to load picard tools~")
JavaTool.__init__(self,
os.path.abspath(jar_path),
tmp_path=os.path.abspath(javatmp),
max_memory=max_memory)
def __init__(self, jar="", javatmp=os.getcwd(), max_memory=None, **kwargs):
if not jar:
raise IOError("Fail to load GATK3 tools~")
JavaTool.__init__(self, os.path.abspath(jar), tmp_path=os.path.abspath(javatmp), max_memory=max_memory)
def __init__(self, jar="snpEff.jar", javatmp=os.getcwd(), max_memory=None):
if not jar:
raise IOError("Fail to load snpEff tools~")
self.jar = os.path.abspath(jar)
JavaTool.__init__(self, self.jar, tmp_path=os.path.abspath(javatmp), max_memory=max_memory)