PileupSpec.hs

module SequenceFormats.PileupSpec (spec) where

import SequenceFormats.Pileup (readPileupFromFile, PileupRow(..), Strand(..))
import SequenceFormats.Utils (Chrom(..))

import Control.Foldl (purely, list)
import qualified Pipes.Prelude as P
import Pipes.Safe (runSafeT)
import Test.Hspec

spec :: Spec
spec = testReadPileupFromFile

testReadPileupFromFile :: Spec
testReadPileupFromFile = describe "readPileupFromFile" $
    it "should read correct data from file" $ do
        let pProd = readPileupFromFile "testDat/example.pileup"
        runSafeT (purely P.fold list pProd) `shouldReturn` mockDatPentries

mockDatPentries :: [PileupRow]
mockDatPentries = [
    PileupRow (Chrom "1") 1000 'A' ["AAACA", "AAAC", "AAAACCAACA"]
        [[f, f, r, f, f], [f, f, r, r], [r, r, f, r, r, r, f, f, r, f]], 
    PileupRow (Chrom "1") 2000 'C' ["CCCA", "ACTCC", "CACACCCC"]
        [[f, f, f, r], [f, f, r, f, f], [f, r, f, r, f, f, f, f]],
    PileupRow (Chrom "2") 1000 'G' ["GGGGGGGCG", "GGG", "GGGGGG"]
        [[r, r, f, r, r, f, f, f, f], [f, r, r], [f, r, r, f, r, r]]]
  where
    f = ForwardStrand
    r = ReverseStrand