#!/usr/bin/env stack

-- stack script --resolver lts-14.1 --package turtle

{-# LANGUAGE OverloadedStrings #-}

import Control.Applicative (optional)

import Prelude hiding (FilePath)

import Turtle

data Options = Options {

optGeno :: FilePath,

optSnp :: FilePath,

optInd :: FilePath,

optPopList :: FilePath,

optLow :: Maybe Int,

optHigh :: Maybe Int

}

main = do

args <- options "Admixtools qpDstat wrapper" parser

runManaged $ do

paramFile <- mktempfile "." "qpDstat_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

let execParams = ["-p", format fp paramFile] ++

maybe [] (\low -> ["-l", format d low]) (optLow args) ++

maybe [] (\high -> ["-h", format d high]) (optHigh args)

ec <- proc "qpDstat" execParams empty

case ec of

ExitSuccess -> return ()

ExitFailure n -> err . unsafeTextToLine $

format ("qpDstat 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"

<*> optional (optInt "lower" 'l' "analyse population quadruples from this line in the popList")

<*> optional (optInt "upper" 'u' "analyse population quadruples up to this line in the popList")