## This code is part of the megaptera package
## © C. Heibl 2016 (last update 2017-10-18)
#' @importFrom ips read.fas write.fas
#' @export
opal.merge <- function(subMSA, merge.exe, mem = "16G"){
## write imput files, then clear from memory
fns <- tempfile(pattern = c("in", "in2", "out"), fileext = ".fas")
write.fas(subMSA[[1]], fns[1])
write.fas(subMSA[[2]], fns[2])
remove(subMSA) ## save memory
## execute opal
system2(command = merge.exe,
args = c(paste("--mem", mem),
paste("--in", fns[1]),
paste("--in2", fns[2]),
paste("--out", fns[3])
)
)
## retrieve output, then remove files
obj <- read.fas(fns[3])
file.remove(fns)
obj
}
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