# Author: Cico Zhang
# Usage: Rscript bum.R --input p-values.txt --output result.txt --verbose TRUE

# Set up R error handling to go to stderr
err_foo <- function() {
  cat(geterrmessage(), file = stderr());
  q("no", 1, F)
}
options(show.error.messages = F, error = err_foo)

# Import required libraries
suppressPackageStartupMessages({
  library("getopt")
  library("BioNet")
})

# Take in trailing command line arguments
args <- commandArgs(trailingOnly = TRUE)

# Get options using the spec as defined by the enclosed list
# Read the options from the default: commandArgs(TRUE)
option_specification <- matrix(c("input", "i", 2, "character",
                                 "output", "o", 2, "character"
                                ), byrow = TRUE, ncol = 4);

# Parse options
options <- getopt(option_specification);

pvals <- read.table(options$input)
bum <- fitBumModel(pvals, plot = FALSE)
mat <- c(bum$lambda, bum$a)
write.table(x = mat, file = options$output, quote = FALSE,
            row.names = FALSE, col.names = FALSE)
message("Parameters have been estimated successfully!")