+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--stranded", action="store_false", dest="ignoreSense")
+ parser.add_option("--uniq", action="store_true", dest="withUniqs")
+ parser.add_option("--multi", action="store_true", dest="withMulti")
+ parser.add_option("--accept", dest="acceptfile")
+ parser.add_option("--cache", type="int", dest="cachePages")
+ parser.add_option("--verbose", action="store_true", dest="doVerbose")
+ parser.add_option("--models", dest="extendGenome")
+ parser.add_option("--replacemodels", action="store_true", dest="replaceModels")
+
+ configParser = getConfigParser()
+ section = "geneMrnaCountsWeighted"
+ ignoreSense = getConfigBoolOption(configParser, section, "ignoreSense", True)
+ withUniqs = getConfigBoolOption(configParser, section, "withUniqs", False)
+ withMulti = getConfigBoolOption(configParser, section, "withMulti", False)
+ acceptfile = getConfigOption(configParser, section, "acceptfile", None)
+ cachePages = getConfigOption(configParser, section, "cachePages", None)
+ doVerbose = getConfigBoolOption(configParser, section, "doVerbose", False)
+ extendGenome = getConfigOption(configParser, section, "extendGenome", "")
+ replaceModels = getConfigBoolOption(configParser, section, "replaceModels", False)
+
+ parser.set_defaults(ignoreSense=ignoreSense, withUniqs=withUniqs, withMulti=withMulti,
+ acceptfile=acceptfile, cachePages=cachePages, doVerbose=doVerbose, extendGenome=extendGenome,
+ replaceModels=replaceModels)
+
+ return parser
+
+
+#TODO: Reported user performance issue. Long run times in conditions:
+# small number of reads ~40-50M
+# all features on single chromosome
+#
+# User states has been a long time problem.
+