bin/run_snv.R

In eyzhao/hrdtools: Homologous Recombination Deficiency Tests with Whole Genome Sequencing

#!/usr/bin/env Rscript

print('loading packages...')
library(optparse)
suppressMessages(library(hrdtools))
print('done')

prepare_optparser <- function(){
#Prepare optparser object. New options will be added in this function first.
    option_list <- list(
        make_option(c("-s","--snv"), type="character", help="SNV file data", dest="snv_file"),
        make_option(c("-g","--genome"), type="character", help="Genome version (default: hg19)", dest="genome", default='hg19')
        )

    optparser <- OptionParser(option_list=option_list,
                              usage="usage: %prog -i <input_file> -s <pi0_file> -c <normal_contamination>",
                              description="Imports necessary data for kaltimer")

    return(optparser)
}

verify_option <- function(options){
# check if mandatory options are present in the options object
    argpass <- TRUE

    if(!file.exists(options$snv_file)){
        argpass <- FALSE
        print("Please provide a valid snv file")
    }

    return(argpass)
}

get_args <- function() {
# Run the argument parser and return arguments
    optparser <- prepare_optparser()
    opt <- parse_args(optparser)
    argpass <- verify_option(opt)
    
    if(!argpass){
       print("Non valid arguments.")
       quit("no", status=1)
    }

    return(opt)
}

if(getOption('run_snv.from.rscript', default=TRUE)) {
    args = get_args()
    run_snv(args$snv_file, args$genome)
}