$	Step-class
$,Step-method	Step-class
$<-	Step-class
$<-,Step-method	Step-class
addEdges	graphMng
addFileSuffix	Utils
argv	Step-class
argv,Step-method	Step-class
checkAllPath	Step-class
checkAllPath,Step-method	Step-class
checkAndInstallBSgenome	runWithFinishCheck
checkAndInstallGenomeFa	runWithFinishCheck
checkAndInstallOrgDb	runWithFinishCheck
checkAndInstallTxDb	runWithFinishCheck
checkFileCreatable	Utils
checkFileExist	Utils
checkPathExist	Utils
checkRequireParam	Step-class
checkRequireParam,Step-method	Step-class
clearStepCache	Step-class
clearStepCache,Step-method	Step-class
configRegName	loadConfig
genReport	Step-class
getAttachedStep	graphMng
getAutoPath	Step-class
getAutoPath,Step-method	Step-class
getBasenamePrefix	Utils
getGenome	setGenome
getJobDir	setJobName
getJobName	setJobName
getNextSteps	graphMng
getObjsInPipe	getObjsInPipe
getParam	Step-class
getParam,Step-method	Step-class
getParamItems	Step-class
getParamItems,Step-method	Step-class
getParamMD5Path	Step-class
getParamMD5Path,Step-method	Step-class
getPathPrefix	Utils
getPipeName	setPipeName
getPrevSteps	graphMng
getRef	setRefDir
getRefDir	setRefDir
getRefFiles	setRefDir
getRefRc	setRefDir
getStepWorkDir	Step-class
getStepWorkDir,Step-method	Step-class
getThreads	setThreads
getTmpDir	setTmpDir
getValidGenome	setGenome
graphMng	graphMng
ignoreCheck	ignoreCheck
init	Step-class
init,Step-method	Step-class
initPipeFrame	initPipeFrame
input	Step-class
input,Step-method	Step-class
input<-	Step-class
input<-,Step-method	Step-class
isReady	Step-class
isReady,Step-method	Step-class
loadConfig	loadConfig
loadStep	loadStep
output	Step-class
output,Step-method	Step-class
output<-	Step-class
output<-,Step-method	Step-class
param	Step-class
param,Step-method	Step-class
param<-	Step-class
param<-,Step-method	Step-class
pipeName	Step-class
pipeName,Step-method	Step-class
printMap	graphMng
processing	Step-class
property	Step-class
property,Step-method	Step-class
property<-	Step-class
property<-,Step-method	Step-class
regAttachedStep	graphMng
report	Step-class
report,Step-method	Step-class
report<-	Step-class
report<-,Step-method	Step-class
runWithFinishCheck	runWithFinishCheck
saveConfig	loadConfig
setGenome	setGenome
setJobName	setJobName
setPipeName	setPipeName
setRefDir	setRefDir
setThreads	setThreads
setTmpDir	setTmpDir
Step	Step-class
Step-class	Step-class
stepID	Step-class
stepID,Step-method	Step-class
stepName	Step-class
stepName,Step-method	Step-class
stepType	Step-class
stepType,Step-method	Step-class
Utils	Utils
writeLog	Step-class
writeLog,Step-method	Step-class
