todo

lions.sh

	line 80: Control script for Cluster/Local runs (Qsub)

initalizeRes.sh
	line 61: self check fails if .fai files aren't provided
	Do full explicit check for them

initializeLIONS.sh
	Check for python3 in bin folder
	Check for bedtools installed

RNAseqPipeline.sh
	
	Add a protocol to change the wig file to UCSC compatible wig files
	I should have conversion scripts on the gsc somewhere

parameter.ctrl

	Split parameter.ctrl into two files;
		A) User set parameters
		B) LIONS internal parameters (SCRIPTS directory etc...)
eastLions.sh

	Core Script: Line 143. When GSC computing is used and ALINGMENTBYPASS =1
	The linked file in ./alignment/ ends up going to /tmp/ instead should
	re-route to the input.list entry for that library
	
	Simplify output files <Library>.lcsv and <Library>.pc.lcsv to a signle
	<Library>.lcsv file (with pc information). These are redundant.

	Add a global paramter to indicate how much virtual memory is used
	especially for JAVA
		RNAseqMaster.sh --> line 95 - 115; -Xmx6G
		ChimericReadTool.sh --> line 237; -Xmx6G
	
	chimSort.R
		for EInside case add First Exon requirements
		for RInside case add UpCov 0.5 requirements


	chimGroup.R
		Increase efficiency of search/match function
	Replace:
	"  Chimera$RMDB  = unlist(lapply(Chimera$RepeatID,
                               FUN=function(Key,Query=RMDB_id){
                                 return(which(Key == Query))}
                )) "
	with:
	"  Chimera$RMDB = unlist(lapply(Chimera$RepeatID[1:1000], match, table = RMDB_id)) "

global

	Add a way to liftOver from a genome to a consensus repeat sequence
	using acrocentric arms of chromosomes as regions in which to contain
	the consensus repeat sequences.