R/bowtie2Version.R

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

# bowtie2Version.R


`checkBowtie2Version` <- function() {

	# if no one has initialized any Bowtie actions, do that first
	bp <- bowtie2Par()
	if ( ! length(bp)) {
		if ( file.exists( "./Options.txt")) {
			bowtie2Par.defaults( optionsFile="./Options.txt", verbose=F)
		} else {
			bowtie2Par.defaults( verbose=F)
		}
	}

	# see if this program is readable and executable
	myProgram <- bowtie2Par( "Program")
	if ( ! (( file.access( myProgram, mode=0) == 0) &&  
		( file.access( myProgram, mode=1) == 0))) {
			cat( "\nCan not execute Bowtie2 version test.  Executable may be missing or not permissioned \n")
			return()
	}

	versionCallCommand <- paste( myProgram, "  --version")
	versionCall <- system( command=versionCallCommand, intern=TRUE)
	terms <- strsplit( versionCall[1], split=" ", fixed=TRUE)[[1]]

	callSuccess <- (terms[2] == "version")
	if ( ! callSuccess) {
		stop( paste( "checkBowtie2Version:  Error:  bowtie2 Program executable version detection failed. \n",
			"Filename as given:  ", bowtie2Par("Program"), "\n",
			"Result: ", versionCall))
	}

	# defaults are based on 'current verison'...  if older, override to whats expected...
	thisVersion <- terms[3]
	assign( "CurrentVersion", value=thisVersion, envir=Bowtie2Env)
	#assign( "NoHitFileOption", value=" --un ", envir=Bowtie2Env)
	#assign( "MultiHitFileOption", value=" --max ", envir=Bowtie2Env)
	return( thisVersion)
}


`getBowtie2Version` <- function() return( get( "CurrentVersion", envir=Bowtie2Env))