# Path: ratatosk/utils.py
# def rreplace(s, old, new, occurrence):
#     li = s.rsplit(old, occurrence)
#     return new.join(li)
# 
# def fullclassname(o):
#     return o.__module__ + "." + o.__name__
# 
# Path: ratatosk/job.py
# class BaseJobTask(luigi.Task):
# class JobTask(BaseJobTask):
# class InputJobTask(JobTask):
# class JobWrapperTask(JobTask):
# class NullJobTask(JobTask):
# class GenericWrapperTask(JobWrapperTask):
# class InputPath(InputJobTask):
# class PipedTask(JobTask):
# class PipelineTask(JobWrapperTask):
# class PrintConfig(JobTask):
#     def __init__(self, *args, **kwargs):
#     def _register_parent_task(self, parents):
#     def _update_config(self, config, param_values_dict, disable_parent_task_update=False, *args, **kwargs):
#     def path(self):
#     def exe(self):
#     def main(self):
#     def opts(self):
#     def args(self):
#     def threads(self):
#     def sfx(self, index=0):
#     def adl(self, index=0):
#     def dil(self, index=0):
#     def lab(self):
#     def max_memory(self):
#     def add_suffix(self):
#     def init_local(self):
#     def run(self):
#     def parent(self):
#     def output(self):
#     def requires(self):
#     def complete(self):
#     def get_param_default(self, k):
#     def target_iterator(self):
#     def source(self):
#     def _make_source_file_name(self, parent_cls, diff_label=None, add_label=None):
#     def job_runner(self):
#     def args(self):
#     def requires(self):
#     def run(self):
#     def complete(self):
#     def run(self):
#     def run(self):
#     def requires(self):
#     def output(self):
#     def job_runner(self):
#     def args(self):
#     def requires(self):
#     def output(self):
#     def run(self):
# def name_prefix():
# def generic_target_generator(target_generator_infile=None, **kwargs):
# 
# Path: ratatosk/log.py
# def get_logger():
#     logger = logging.getLogger('ratatosk-interface')
#     if not logger.handlers:
#         setup_logging()
#     return logger


import os
import luigi
import logging
import ratatosk.lib.files.input
import ratatosk.shell as shell
from ratatosk.utils import rreplace, fullclassname
from ratatosk.job import JobTask, DefaultShellJobRunner
from ratatosk.log import get_logger
# Copyright (c) 2013 Per Unneberg
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations under
# the License.
"""
Provide wrappers for `mutect <http://www.broadinstitute.org/cancer/cga/mutect>`_


Classes
-------
"""



# Path: ratatosk/utils.py
# def rreplace(s, old, new, occurrence):
#     li = s.rsplit(old, occurrence)
#     return new.join(li)
# 
# def fullclassname(o):
#     return o.__module__ + "." + o.__name__
# 
# Path: ratatosk/job.py
# class BaseJobTask(luigi.Task):
# class JobTask(BaseJobTask):
# class InputJobTask(JobTask):
# class JobWrapperTask(JobTask):
# class NullJobTask(JobTask):
# class GenericWrapperTask(JobWrapperTask):
# class InputPath(InputJobTask):
# class PipedTask(JobTask):
# class PipelineTask(JobWrapperTask):
# class PrintConfig(JobTask):
#     def __init__(self, *args, **kwargs):
#     def _register_parent_task(self, parents):
#     def _update_config(self, config, param_values_dict, disable_parent_task_update=False, *args, **kwargs):
#     def path(self):
#     def exe(self):
#     def main(self):
#     def opts(self):
#     def args(self):
#     def threads(self):
#     def sfx(self, index=0):
#     def adl(self, index=0):
#     def dil(self, index=0):
#     def lab(self):
#     def max_memory(self):
#     def add_suffix(self):
#     def init_local(self):
#     def run(self):
#     def parent(self):
#     def output(self):
#     def requires(self):
#     def complete(self):
#     def get_param_default(self, k):
#     def target_iterator(self):
#     def source(self):
#     def _make_source_file_name(self, parent_cls, diff_label=None, add_label=None):
#     def job_runner(self):
#     def args(self):
#     def requires(self):
#     def run(self):
#     def complete(self):
#     def run(self):
#     def run(self):
#     def requires(self):
#     def output(self):
#     def job_runner(self):
#     def args(self):
#     def requires(self):
#     def output(self):
#     def run(self):
# def name_prefix():
# def generic_target_generator(target_generator_infile=None, **kwargs):
# 
# Path: ratatosk/log.py
# def get_logger():
#     logger = logging.getLogger('ratatosk-interface')
#     if not logger.handlers:
#         setup_logging()
#     return logger


# Path: ratatosk/lib/cancer/mutect.py
import os
import luigi
import logging
import ratatosk.lib.files.input
import ratatosk.shell as shell
from ratatosk.utils import rreplace, fullclassname
from ratatosk.job import JobTask, DefaultShellJobRunner
from ratatosk.log import get_logger

# Copyright (c) 2013 Per Unneberg
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
# WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
# License for the specific language governing permissions and limitations under
# the License.
"""
Provide wrappers for `mutect <http://www.broadinstitute.org/cancer/cga/mutect>`_


Classes
-------
"""



logger = get_logger()