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)
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)
