+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--multifraction", action="store_true", dest="reportfraction")
+ parser.add_option("--multifold", action="store_true", dest="reportFold")
+ parser.add_option("--minrpkm", type="float", dest="minThreshold")
+ parser.add_option("--cache", action="store_true", dest="doCache")
+ parser.add_option("--withGID", action="store_true", dest="writeGID")
+
+ configParser = getConfigParser()
+ section = "normalizeFinalExonic"
+ reportFraction = getConfigBoolOption(configParser, section, "multifraction", False)
+ reportFold = getConfigBoolOption(configParser, section, "reportFold", False)
+ minThreshold = getConfigFloatOption(configParser, section, "minThreshold", 0.)
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+ writeGID = getConfigBoolOption(configParser, section, "writeGID", False)
+
+ parser.set_defaults(reportFraction=reportFraction, reportFold=reportFold, minThreshold=minThreshold,
+ doCache=doCache, writeGID=writeGID)
+
+ return parser
+
+