#!/usr/bin/env Rscript
suppressPackageStartupMessages(library("optparse"))
option_list <- list(
make_option(c("-c", "--contig_folder"), help="Contig folder"),
make_option(c("-r", "--ref_folder"), help="Reference folder"),
make_option(c("-n", "--name_file"), help="consensus fasta name scheme file"),
make_option(c("-o", "--out_folder"), help="output folder"),
make_option(c("-f", "--filter"), help="TRUE or FALSE, perform read number filter or not"),
make_option(c("-p", "--percentage"), help="below the specific percentage of read number will be filter, only effective when --filter=TRUE")
)
opt <- parse_args(OptionParser(option_list=option_list))
suppressPackageStartupMessages(library("skleid"))
autoReport(opt$contig_folder, opt$ref_folder, opt$name_file, opt$out_folder, opt$filter, opt$percentage)
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