## How to execute this tool

# A command-line interface to lineagespot for use with Galaxy
#
# The following arguments are required:
#
# 'in_vcf'  a character vector of paths to VCF files object from Galaxy lineagespot/test-data
# 'in_gff3' a character vector of path to GFF3 file containing SARS-CoV-2 gene coordinates object from Galaxy lineagespot/test-data
# 'in_ref'  a character vector of path to a folder containing lineage reports object from Galaxy lineagespot/test-data
# 'in_voc'  a character vector containing the names of the lineages of interest
# 'in_threshold' a parameter indicating the AF threshold for identifying variants per sample
#
# Rscript ${__tool_directory__}/lineagespot_verbose.R --in_vcf ${__tool_directory__}/test-data/extdata/vcf-files --in_gff3 ${__tool_directory__}/test-data/extdata/NC_045512.2_annot.gff3 --in_ref ${__tool_directory__}/test-data/extdata/ref --in_voc "B.1.617.2, B.1.1.7, B.1.351, P.1" --in_threshold 0.8
# Set up R error handling to go to stderr
options(show.error.messages = FALSE, error = function() {
    cat(geterrmessage(), file = stderr())
    q("no", 1, FALSE)
})

# Import required libraries

library_path <- .libPaths()

suppressPackageStartupMessages({
    library("getopt", lib.loc = library_path)
    library("data.table", lib.loc = library_path)
    library("lineagespot", lib.loc = library_path)
})


options(stringAsfactors = FALSE, useFancyQuotes = FALSE)

# 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(
    "in_vcf", "vcf", 1, "character",
    "in_gff3", "gff3", 1, "character",
    "in_ref", "ref", 1, "character",
    "in_voc", "voc", 2, "character",
    "in_threshold", "thr", 2, "double"
), byrow = TRUE, ncol = 4)

options <- getopt(option_specification)

if (!is.null(options$in_voc) && is.character(options$in_voc)) {
    options$in_voc <- unlist(strsplit(options$in_voc, split = ","))
}

result <- lineagespot(
    vcf_folder = options$in_vcf,
    ref_folder = options$in_ref,
    gff3_path = options$in_gff3,
    voc = options$in_voc,
    AF_threshold = options$in_threshold
)


# Write output to new file which will be recognized by Galaxy
fwrite(result$variants.table, sep = "\t", file = "variants_table.txt", row.names = FALSE)
fwrite(result$lineage.hits, sep = "\t", file = "lineage_hits.txt", row.names = FALSE)
fwrite(result$lineage.report, sep = "\t", file = "lineage_report.txt", row.names = FALSE)

cat("\n Process has been completed !\n")