def registerCustomExecutables(self, workflow): """ 2011-11-28 """ FilterVCFPipeline.registerCustomExecutables(self, workflow) namespace = workflow.namespace version = workflow.version operatingSystem = workflow.operatingSystem architecture = workflow.architecture clusters_size = workflow.clusters_size site_handler = workflow.site_handler vervetSrcPath = self.vervetSrcPath
def __init__(self, **keywords):
"""
"""
FilterVCFPipeline.__init__(self, **keywords)
self.inputDir = os.path.abspath(self.inputDir)
listArgumentName_data_type_ls = [('depthFoldChangeLs', int), ("minDepthPerGenotypeLs", int), \
("minMACLs", int), ("minMAFLs", float), ("maxSNPMissingRateLs", float)]
listArgumentName2hasContent = self.processListArguments(listArgumentName_data_type_ls, emptyContent=[None])
if listArgumentName2hasContent['depthFoldChangeLs'] and not self.alnStatForFilterFname:
sys.stderr.write("Error: alnStatForFilterFname (%s) is nothing while depthFoldChangeLs=%s.\n"%\
(self.alnStatForFilterFname, repr(self.depthFoldChangeLs)))
sys.exit(3)
def __init__(self, **keywords): """ """ FilterVCFPipeline.__init__(self, **keywords)