+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--append", action="store_false", dest="init",
+ help="append to existing rds file [default: create new]")
+ parser.add_option("--RNA", action="store_true", dest="rnaDataType",
+ help="set data type to RNA [default: DNA]")
+ parser.add_option("-S", "--sam", action="store_true", dest="useSamFile",
+ help="input file is in sam format")
+ parser.add_option("--index", action="store_true", dest="doIndex",
+ help="index the output rds file")
+ parser.add_option("--cache", type="int", dest="cachePages",
+ help="number of cache pages to use [default: 100000")
+ parser.add_option("-m", "--multiCount", type="int", dest="maxMultiReadCount",
+ help="multi counts over this value are discarded [default: 10]")
+ parser.add_option("--rawreadID", action="store_false", dest="trimReadID",
+ help="use the raw read names")
+
+ configParser = getConfigParser()
+ section = "makeRdsFromBam"
+ init = getConfigBoolOption(configParser, section, "init", True)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ useSamFile = getConfigBoolOption(configParser, section, "useSamFile", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+ maxMultiReadCount = getConfigIntOption(configParser, section, "maxMultiReadCount", 10)
+ rnaDataType = getConfigBoolOption(configParser, section, "rnaDataType", False)
+ trimReadID = getConfigBoolOption(configParser, section, "trimReadID", True)
+
+ parser.set_defaults(init=init, doIndex=doIndex, useSamFile=useSamFile, cachePages=cachePages,
+ maxMultiReadCount=maxMultiReadCount, rnaDataType=rnaDataType, trimReadID=trimReadID)
+
+ return parser
+
+