def _validate(self, params):
samt = SamTools(self.config, self.__LOGGER)
if 'ignore' in params:
path, file = os.path.split(params['file_path'])
rval = samt.validate(ifile=file,
ipath=path,
ignore=params['ignore'])
else:
path, file = os.path.split(params['file_path'])
rval = samt.validate(ifile=file, ipath=path)
return rval
def test_invalid_validate(self):
samt = SamTools(self.__class__.cfg, self.__class__.__LOGGER)
rval = samt.validate(ifile='accepted_hits_invalid.sam',
ipath='/kb/module/test/data/samtools')
self.assertEquals(1, rval)
def test_valid_validate(self):
samt = SamTools(self.__class__.cfg, self.__class__.__LOGGER)
rval = samt.validate(ifile='accepted_hits.sam',
ipath='/kb/module/test/data/samtools',
ignore=['MISSING_READ_GROUP'])
self.assertEquals(0, rval)