#!/usr/bin/env stack

{-# LANGUAGE OverloadedStrings #-}

import Control.Applicative (optional)

import Prelude hiding (FilePath)

import Turtle

data Options = Options {

optGeno :: FilePath,

optSnp :: FilePath,

optInd :: FilePath,

optPopList :: FilePath

main = do

args <- options "Admixtools qp3Pop wrapper" parser

runManaged $ do

paramFile <- mktempfile "." "qp3Pop_wrapper"

let content = [(format ("genotypename:\t"%fp) (optGeno args)),

(format ("snpname:\t"%fp) (optSnp args)),

(format ("indivname:\t"%fp) (optInd args)),

(format ("popfilename:\t"%fp) (optPopList args))]

output paramFile . select . map unsafeTextToLine $ content

ec <- proc "qp3Pop" ["-p", format fp paramFile] empty

case ec of

ExitSuccess -> return ()

ExitFailure n -> err . unsafeTextToLine $ format ("qp3Pop failed with exit code "%d) n

parser :: Parser Options

parser = Options <$> optPath "geno" 'g' "Genotype File"

<*> optPath "snp" 's' "Snp File"

<*> optPath "ind" 'i' "Ind File"

<*> optPath "popList" 'p' "give a list with all population triples"