#' @export
runDetect <- function(inp.pth, cfg.pth) {
beg.time <- Sys.time()
##
ann <- readRDS(cfg.pth)
## annotation / configuration
if (packageVersion("codac")[,1:2] != ann$par$version[,1:2]) {
write("Configuration and program version mismatch.\n", stderr())
quit("no", 1)
}
dir <- makeDirectory(inp.pth)
cts <- readCounts(dir, ann)
spl <- readSplices(dir, ann)
jnc <- readJunctions(dir, ann)
bpt <- collapseBreakpoints(jnc, ann)
stat <- makeStat(jnc, bpt, spl, dir, ann)
bun <- makeBundle(bpt, jnc, "full")
end.time <- Sys.time()
stat$log$beg.time <- beg.time
stat$log$end.time <- end.time
stat$log$gc <- gc()
run <- list(ann=ann, dir=dir, cts=cts, spl=spl, stat=stat, bun=bun)
return(run)
}
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