- makewiggle(name, hitfilename, outfilename, options.doNormalize, options.color, options.altColor,
- options.limitChrom, options.shift, options.doSplit, options.listfilename, options.listPrefix,
- options.group, options.startPriority, options.skipRandom, options.withMulti,
- options.withSplices, options.doSingle, options.cachePages, options.enforceChr, options.strand,
- options.chunk)
+ configParser = getConfigParser()
+ section = "makewiggle"
+ doNormalize = getConfigBoolOption(configParser, section, "doNormalize", True)
+ color = getConfigOption(configParser, section, "color", None)
+ altColor = getConfigOption(configParser, section, "altColor", "")
+ limitChrom = getConfigOption(configParser, section, "limitChrom", None)
+ shift = getConfigIntOption(configParser, section, "shift", 0)
+ doSplit = getConfigBoolOption(configParser, section, "doSplit", False)
+ listfilename = getConfigOption(configParser, section, "listfilename", None)
+ listPrefix = getConfigOption(configParser, section, "listPrefix", "")
+ group = getConfigOption(configParser, section, "group", "")
+ startPriority = getConfigFloatOption(configParser, section, "startPriority", 0.01)
+ skipRandom = getConfigBoolOption(configParser, section, "skipRandom", False)
+ withMulti = getConfigBoolOption(configParser, section, "withMulti", True)
+ withSplices = getConfigBoolOption(configParser, section, "withSplices", False)
+ doSingle = getConfigBoolOption(configParser, section, "doSingle", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", -1)
+ enforceChr = getConfigBoolOption(configParser, section, "enforceChr", False)
+ strand = getConfigOption(configParser, section, "strand", None)
+ chunk = getConfigIntOption(configParser, section, "chunk", 20)
+
+ parser.set_defaults(doNormalize=doNormalize, color=color, altColor=altColor, limitChrom=limitChrom,
+ shift=shift, doSplit=doSplit, listfilename=listfilename, listPrefix=listPrefix,
+ group=group, startPriority=startPriority, skipRandom=skipRandom, withMulti=withMulti,
+ withSplices=withSplices, doSingle=doSingle, cachePages=cachePages, enforceChr=enforceChr,
+ strand=strand, chunk=chunk)
+
+ return parser