#' gather alignment statistic on a directory of star alignments
#'
#' @param projName project names
#' @param fileList list of log files
#' @param locDir location for (temporary) local storage of log files
#'
#' @export
summariseSubread <- function(projName,fileList, locDir="/Users/pschofield/.tmp"){
ret <- lapply(fileList,function(fn){
tmpFile <- plib::getFiles(filenames=basename(fn),
remDir=gsub("/scratch/","",dirname(fn)),
locDir=gsub("/Users/","",locDir))
res <- read.delim(file.path(locDir,basename(fn)),sep="\t",head=F,row.names=1,stringsAsFactors=F)
rownames(res) <- gdata::trim(gsub("([:]|[(]|[)])","",rownames(res)))
rownames(res) <- gsub("([ ]|[-])","_",rownames(res))
t(res)
})
names(ret) <- gsub("[.]stats$","",basename(fileList))
ret <- plyr::ldply(ret)
rownames(ret) <- ret[,1]
ret$percent_mapped <- ret$reads_mapped/srSummary$sequences
ret$percent_multimapped <- ret$non_primary_alignment/srSummary$sequences
ret[,-1]
}
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