#' bank_reads
#'
#' JAMSalpha function
#' @export
bank_reads<-function(opt=opt){
#Check if reads are in tmpdir
if(opt$workdir != opt$sampledir){
readsworkdir<-file.path(opt$workdir, "reads")
} else {
readsworkdir<-opt$readsdir
}
setwd(readsworkdir)
if(opt$host != "none"){
flog.info("Banking Non-Aligned to Host Species (microbiota) reads to outdir.")
fastqstobank<-opt$nahsreads
outfilename<-paste(paste(opt$prefix, "Microbiota", "reads", sep="_"), "tar", "gz", sep=".")
} else {
flog.info("Banking QC trimmed reads to outdir.")
fastqstobank<-opt$trimreads
outfilename<-paste(paste(opt$prefix, "QCtrimmed", "reads", sep="_"), "tar", "gz", sep=".")
}
outfilepath <- file.path(opt$outdir, outfilename)
tarcmd<-paste("tar", "cf", "-", paste0(fastqstobank, collapse=" "), "|", "pigz", "-9", "-p", opt$threads, ">", outfilepath, collapse=" ")
system(tarcmd)
}
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