+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--sameChrom", action="store_true", dest="sameChromOnly")
+ parser.add_option("--splices", action="store_true", dest="doSplices")
+ parser.add_option("--verbose", action="store_true", dest="doVerbose")
+ parser.add_option("--maxDist", type="int", dest="maxDist")
+ parser.add_option("--cache", type="int", dest="cachePages")
+
+ configParser = getConfigParser()
+ section = "distalPairs"
+ sameChromOnly = getConfigBoolOption(configParser, section, "sameChromOnly", False)
+ doSplices = getConfigBoolOption(configParser, section, "doSplices", False)
+ doVerbose = getConfigBoolOption(configParser, section, "doVerbose", False)
+ maxDist = getConfigIntOption(configParser, section, "maxDist", 1000000000)
+ cachePages = getConfigOption(configParser, section, "cachePages", None)
+
+ parser.set_defaults(sameChromOnly=sameChromOnly, doSplices=doSplices, doVerbose=doVerbose, maxDist=maxDist, cachePages=cachePages)
+
+ return parser
+
+