#!/bin/bash
# -*- mode: julia -*-
#=
exec julia --project="$(realpath "$(dirname "${BASH_SOURCE[0]}")")" "${BASH_SOURCE[0]}" "$@"
=#
# beefblup cli
# Provides a convenient CLI for using beefblup
# cSpell:includeRegExp #.*
# cSpell:includeRegExp ("""|''')[^\1]*\1

# Import packages
using BeefBLUP
using ArgParse

# If this is run without arguments, catch that before parsing
if isempty(ARGS)
    BeefBLUP.beefblup()
    exit()
end

# Setup the argument table
argsettings = ArgParseSettings()
@add_arg_table argsettings begin
    "datafile"
        help = "datasheet containing the pedigree, fixed effects, and response trait formatted in CSV"
        required = true
        arg_type = String
    "resultsfile"
        help = "filename for storing the results of the analysis"
        required = false
        arg_type = String
    "--heritability", "-t"
        help = "heritability of the response trait being analyzed"
        required = true
        arg_type = Float64
end

arguments = parse_args(argsettings)

h2 = arguments["heritability"]

if isnothing(arguments["resultsfile"])
    BeefBLUP.beefblup(arguments["datafile"], h2)
    exit()
end

BeefBLUP.beefblup(arguments["datafile"], arguments["resultsfile"], h2)