bioinformatics-toolkit 0.9.5 → 0.10.0

raw patch · 14 files changed

+224/−305 lines, 14 filesdep +deepseqdep ~aesondep ~attoparsecbinary-addedPVP ok

version bump matches the API change (PVP)

Dependencies added: deepseq

Dependency ranges changed: aeson, attoparsec

API changes (from Hackage documentation)

Files

• benchmarks/bench.hs +19/−10
• bioinformatics-toolkit.cabal +8/−5
• src/Bio/Data/Bam.hs +0/−1
• src/Bio/Data/Bed/Types.hs +43/−39
• src/Bio/Data/Bed/Utils.hs +28/−6
• src/Bio/Data/Fastq.hs +92/−20
• src/Bio/GO.hs +0/−2
• src/Bio/RealWorld/ENCODE.hs +4/−2
• src/Bio/RealWorld/Ensembl.hs +1/−1
• src/Bio/Utils/Functions.hs +12/−12
• tests/Tests/Fastq.hs +17/−7
• tests/data/test.fastq +0/−200
• tests/data/test.fastq.gz binary
• tests/data/test_wrap.fastq.gz binary

@@ -2,22 +2,24 @@  import Criterion.Main import System.Random+import Data.Conduit.Zlib (ungzip, multiple, gzip) import qualified Data.ByteString.Char8 as B import Data.Default.Class-import qualified Data.Conduit.List as CL-import Data.Conduit+import Conduit import Control.Monad.Identity import System.IO.Unsafe import AI.Clustering.Hierarchical+import Data.Either  import Bio.Data.Fasta+import Bio.Data.Fastq import Bio.Motif import Bio.Motif.Search import Bio.Motif.Alignment import Bio.Seq  dna :: DNA Basic-dna = fromBS $ B.pack $ map f $ take 5000 $ randomRs (0, 3) (mkStdGen 2)+dna = fromRight undefined $ fromBS $ B.pack $ map f $ take 5000 $ randomRs (0, 3) (mkStdGen 2)   where     f :: Int -> Char     f x = case x of@@ -44,10 +46,17 @@ motifs = unsafePerformIO $ readFasta' "data/motifs.fasta"  main :: IO ()-main = defaultMain -    [ bench "motif score" $ nf (scores def pwm) dna -    , bgroup "TFBS scanning" [ bench "Naive" $ nf (\x -> runIdentity $ findTFBSSlow def pwm x (0.6 * optimalScore def pwm) $$ CL.consume) dna-                             , bench "look ahead" $ nf (\x -> runIdentity $ findTFBS def pwm x (0.6 * optimalScore def pwm) $$ CL.consume) dna-                             ]-    , bench "motif merge" $ nf (\x -> fmap show $ flatten $ buildTree x) motifs-    ]+main = do+  content <- fmap B.concat $ runResourceT $ runConduit $+      sourceFile "tests/data/test.fastq.gz" .| multiple ungzip .| sinkList+  let fq = B.concat $ replicate 50 content+  defaultMain +      [ bench "motif score" $ nf (scores def pwm) dna +      --, bgroup "TFBS scanning" [ bench "Naive" $ nf (\x -> runIdentity $ findTFBSSlow def pwm x (0.6 * optimalScore def pwm) $$ CL.consume) dna+      --                         , bench "look ahead" $ nf (\x -> runIdentity $ findTFBS def pwm x (0.6 * optimalScore def pwm) $$ CL.consume) dna+      --                         ]+      --, bench "motif merge" $ nf (\x -> fmap show $ flatten $ buildTree x) motifs+      , bench "Read FASTQ Fast" $ nfAppIO (\x -> runConduit $ yield x .| parseFastqC .| sinkList) fq+      , bench "Read FASTQ Slow" $ nfAppIO (\x -> runConduit $ yield x .| parseFastqC' .| sinkList) fq+      ]+

@@ -1,5 +1,5 @@ name:                bioinformatics-toolkit-version:             0.9.5+version:             0.10.0 synopsis:            A collection of bioinformatics tools description:         A collection of bioinformatics tools license:             MIT@@ -10,7 +10,7 @@ category:            Bio build-type:          Simple extra-source-files:  README.md-cabal-version:       >=1.18+cabal-version:       1.18 data-files:   tests/data/example.bam   tests/data/example.bed.gz@@ -21,7 +21,8 @@   tests/data/example_intersect_peaks.bed.gz   tests/data/motifs.fasta   tests/data/motifs.meme-  tests/data/test.fastq+  tests/data/test.fastq.gz+  tests/data/test_wrap.fastq.gz   tests/data/genes.gtf.gz  library@@ -60,9 +61,9 @@    build-depends:       base >=4.11 && <5.0-    , aeson+    , aeson >= 2.0     , aeson-pretty-    , attoparsec+    , attoparsec >= 0.13.0.0     , bytestring >= 0.10     , bytestring-lexing >= 0.5     , case-insensitive@@ -73,6 +74,7 @@     , data-ordlist     , data-default-class     , double-conversion+    , deepseq     , HsHTSLib >= 1.9.2     , http-conduit >= 2.1.8     , hexpat@@ -108,6 +110,7 @@     , bytestring     , data-default-class     , conduit+    , conduit-extra     , mtl  test-suite tests

@@ -17,7 +17,6 @@ import Control.Monad (mzero) import Data.List (foldl') import           Bio.Data.Bed-import           Bio.Data.Bed.Types import           Bio.Data.Fastq import           Bio.HTS import           Conduit

@@ -1,5 +1,7 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE TemplateHaskell #-}+{-# LANGUAGE StrictData #-}+{-# LANGUAGE DeriveGeneric, DeriveAnyClass #-}  module Bio.Data.Bed.Types     ( BEDLike(..)@@ -32,6 +34,8 @@ import qualified Data.HashMap.Strict               as M import qualified Data.IntervalMap.Strict           as IM import           Data.Maybe                        (fromJust, fromMaybe)+import GHC.Generics (Generic)+import Control.DeepSeq (NFData)  import           Bio.Utils.Misc                    (readDouble, readInt) @@ -87,13 +91,13 @@  -- | BED6 format, as described in http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7 data BED = BED-    { _bed_chrom      :: !B.ByteString-    , _bed_chromStart :: !Int-    , _bed_chromEnd   :: !Int-    , _bed_name       :: !(Maybe B.ByteString)-    , _bed_score      :: !(Maybe Int)-    , _bed_strand     :: !(Maybe Bool)  -- ^ True: "+", False: "-"-    } deriving (Eq, Show, Read)+    { _bed_chrom      :: B.ByteString+    , _bed_chromStart :: Int+    , _bed_chromEnd   :: Int+    , _bed_name       :: Maybe B.ByteString+    , _bed_score      :: Maybe Int+    , _bed_strand     :: Maybe Bool  -- ^ True: "+", False: "-"+    } deriving (Eq, Show, Read, Generic, NFData)  instance Ord BED where     compare (BED x1 x2 x3 x4 x5 x6) (BED y1 y2 y3 y4 y5 y6) =@@ -149,10 +153,10 @@  -- | BED3 format data BED3 = BED3-    { _bed3_chrom       :: !B.ByteString-    , _bed3_chrom_start :: !Int-    , _bed3_chrom_end   :: !Int-    } deriving (Eq, Show, Read)+    { _bed3_chrom       :: B.ByteString+    , _bed3_chrom_start :: Int+    , _bed3_chrom_end   :: Int+    } deriving (Eq, Show, Read, Generic, NFData)  instance Ord BED3 where     compare (BED3 x1 x2 x3) (BED3 y1 y2 y3) = compare (x1,x2,x3) (y1,y2,y3)@@ -179,11 +183,11 @@  -- | Bedgraph format. data BEDGraph = BEDGraph-    { _bdg_chrom       :: !B.ByteString-    , _bdg_chrom_start :: !Int-    , _bdg_chrom_end   :: !Int-    , _bdg_value       :: !Double-    } deriving (Eq, Show, Read)+    { _bdg_chrom       :: B.ByteString+    , _bdg_chrom_start :: Int+    , _bdg_chrom_end   :: Int+    , _bdg_value       :: Double+    } deriving (Eq, Show, Read, Generic, NFData)  makeLensesFor [("_bdg_value", "bdgValue")] ''BEDGraph @@ -215,17 +219,17 @@  -- | ENCODE narrowPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format12 data NarrowPeak = NarrowPeak-    { _npChrom  :: !B.ByteString-    , _npStart  :: !Int-    , _npEnd    :: !Int-    , _npName   :: !(Maybe B.ByteString)-    , _npScore  :: !Int-    , _npStrand :: !(Maybe Bool)-    , _npSignal  :: !Double-    , _npPvalue :: !(Maybe Double)-    , _npQvalue :: !(Maybe Double)-    , _npPeak   :: !(Maybe Int)-    } deriving (Eq, Show, Read)+    { _npChrom  :: B.ByteString+    , _npStart  :: Int+    , _npEnd    :: Int+    , _npName   :: Maybe B.ByteString+    , _npScore  :: Int+    , _npStrand :: Maybe Bool+    , _npSignal :: Double+    , _npPvalue :: Maybe Double+    , _npQvalue :: Maybe Double+    , _npPeak   :: Maybe Int+    } deriving (Eq, Show, Read, Generic, NFData)  makeLensesFor [ ("_npSignal", "npSignal")               , ("_npPvalue", "npPvalue")@@ -276,16 +280,16 @@  -- | ENCODE broadPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format13 data BroadPeak = BroadPeak-    { _bpChrom  :: !B.ByteString-    , _bpStart  :: !Int-    , _bpEnd    :: !Int-    , _bpName   :: !(Maybe B.ByteString)-    , _bpScore  :: !Int-    , _bpStrand :: !(Maybe Bool)-    , _bpSignal  :: !Double-    , _bpPvalue :: !(Maybe Double)-    , _bpQvalue :: !(Maybe Double)-    } deriving (Eq, Show, Read)+    { _bpChrom  :: B.ByteString+    , _bpStart  :: Int+    , _bpEnd    :: Int+    , _bpName   :: Maybe B.ByteString+    , _bpScore  :: Int+    , _bpStrand :: Maybe Bool+    , _bpSignal :: Double+    , _bpPvalue :: Maybe Double+    , _bpQvalue :: Maybe Double+    } deriving (Eq, Show, Read, Generic, NFData)  makeLensesFor [ ("_bpSignal", "bpSignal")               , ("_bpPvalue", "bpPvalue")@@ -333,7 +337,7 @@ data BEDExt bed a = BEDExt     { _ext_bed :: bed     , _ext_data :: a-    } deriving (Eq, Show, Read)+    } deriving (Eq, Show, Read, Generic, NFData)  makeLensesFor [("_ext_bed", "_bed"), ("_ext_data", "_data")] ''BEDExt @@ -346,7 +350,7 @@     strand = _bed . strand  instance (Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a) where-    asBed chr s e = BEDExt (asBed chr s e) $ error "data not available"+    asBed _ _ _ = error "Unable to transform arbitrary record to BEDExt"      fromLine l = let (a, b) = B.breakEnd (=='\t') l                  in BEDExt (fromLine $ B.init a) $ read $ B.unpack b

@@ -16,6 +16,7 @@     , queryBaseMap     , rpkmBed     , rpkmSortedBed+    , countTagsBed     , countTagsBinBed     , countTagsBinBed'     , tagCountDistr@@ -176,11 +177,11 @@                    V.unsafeFreeze v'     let (idx, sortedRegions) = V.unzip v         n = G.length idx-    rc <- rpkmSortedBed $ Sorted sortedRegions+    readCount <- rpkmSortedBed $ Sorted sortedRegions      lift $ do         result <- GM.new n-        G.sequence_ . G.imap (\x i -> GM.unsafeWrite result i (rc U.! x)) $ idx+        G.sequence_ . G.imap (\x i -> GM.unsafeWrite result i (readCount U.! x)) $ idx         G.unsafeFreeze result {-# INLINE rpkmBed #-} @@ -210,6 +211,27 @@     l = G.length regions {-# INLINE rpkmSortedBed #-} +countTagsBed :: (PrimMonad m, BEDLike b, G.Vector v Int)+             => [b] -> ConduitT BED o m (v Int, Int)+countTagsBed regions = do+    vec <- lift $ GM.replicate l 0+    n <- foldMC (count vec) (0 :: Int)+    vec' <- lift $ G.unsafeFreeze vec+    return (vec', n)+  where+    count v nTags tag = do+        let p | tag^.strand == Just True = tag^.chromStart+              | tag^.strand == Just False = tag^.chromEnd - 1+              | otherwise = error "Unkown strand"+            xs = concat $ IM.elems $+                IM.containing (M.lookupDefault IM.empty (tag^.chrom) intervalMap) p+        addOne v xs+        return $ succ nTags+    intervalMap = bedToTree (++) $ zip regions $ map return [0..]+    addOne v' = mapM_ $ \x -> GM.unsafeRead v' x >>= GM.unsafeWrite v' x . (+1)+    l = length regions+{-# INLINE countTagsBed #-}+ -- | divide each region into consecutive bins, and count tags for each bin and -- return the number of all tags. Note: a tag is considered to be overlapped -- with a region only if the starting position of the tag is in the region. For@@ -226,8 +248,8 @@         v <- GM.replicate num 0         return (v, index)     nTags <- foldMC (f vs) 0-    rc <- lift $ mapM (G.unsafeFreeze . fst) $ G.toList vs-    return (rc, nTags)+    readCount <- lift $ mapM (G.unsafeFreeze . fst) $ G.toList vs+    return (readCount, nTags)   where     f vs n bed = do         let pos | bed^.strand == Just True = bed^.chromStart@@ -282,8 +304,8 @@                         GM.unsafeRead v i >>= GM.unsafeWrite v i . (+1)                 sink (nTags+1) vs -            _ -> do rc <- lift $ mapM (G.unsafeFreeze . fst) $ G.toList vs-                    return (rc, nTags)+            _ -> do readCount <- lift $ mapM (G.unsafeFreeze . fst) $ G.toList vs+                    return (readCount, nTags)      intervalMap = bedToTree (++) $ zip beds $ map return [0..] {-# INLINE countTagsBinBed' #-}

@@ -1,5 +1,6 @@ {-# LANGUAGE LambdaCase #-} {-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE DeriveGeneric, DeriveAnyClass #-} module Bio.Data.Fastq     ( Fastq(..)     , streamFastqGzip@@ -7,6 +8,7 @@     , sinkFastqGzip     , sinkFastq     , parseFastqC+    , parseFastqC'     , fastqToByteString     , qualitySummary     , trimPolyA@@ -19,6 +21,8 @@ import qualified Data.Attoparsec.ByteString as A import Data.Attoparsec.ByteString.Char8 import Data.Conduit.Attoparsec+import GHC.Generics (Generic)+import Control.DeepSeq  -- | A FASTQ file normally uses four lines per sequence. --@@ -36,7 +40,7 @@     { fastqSeqId   :: B.ByteString     , fastqSeq     :: B.ByteString     , fastqSeqQual :: B.ByteString-    } deriving (Show, Eq)+    } deriving (Show, Eq, Generic, NFData)  -- | Read gzipped fastq file. streamFastqGzip :: (PrimMonad m, MonadThrow m, MonadResource m) @@ -55,29 +59,97 @@               => FilePath -> ConduitT Fastq o m () sinkFastqGzip fl = mapC fastqToByteString .| unlinesAsciiC .| gzip .| sinkFileBS fl -parseFastqC :: MonadThrow m => ConduitT B.ByteString Fastq m ()-parseFastqC = conduitParser fastqParser .| mapC snd+data FQBuilder = Init FQBuilder+               | FQ1 B.ByteString FQBuilder+               | FQ2 B.ByteString FQBuilder+               | FQ3 B.ByteString FQBuilder+               | Complete++fqBuilder :: FQBuilder -> Fastq+fqBuilder = go ([], [], [])+  where+    go acc (Init bldr) = go acc bldr+    go (f1,f2,f3) (FQ1 x bldr) = go (x:f1, f2, f3) bldr+    go (f1,f2,f3) (FQ2 x bldr) = go (f1, x:f2, f3) bldr+    go (f1,f2,f3) (FQ3 x bldr) = go (f1, f2, x:f3) bldr+    go (f1,f2,f3) Complete = Fastq (B.concat $ reverse f1)+        (B.concat $ reverse f2) (B.concat $ reverse f3)+{-# INLINE fqBuilder #-}++parseFastqC :: Monad m => ConduitT B.ByteString Fastq m ()+parseFastqC = await >>= maybe (error "Empty input") ( \x -> do+    if B.head x == '@'+        then loop Init 'a' $ B.tail x+        else error "Record does not start with \'@\'" )+  where+    tryRead1 input | B.null input = await >>= maybe (error "Unexpected EOF") return+                   | otherwise = return input+    loop acc st input = case st of+        'a' -> do+            (x, rest) <- B.break (=='\n') <$> tryRead1 input+            if B.null rest+                then loop (acc . FQ1 x) 'a' rest+                else loop (acc . FQ1 x) 'b' $ B.tail rest+        'b' -> do +            (x, rest) <- B.break (=='\n') <$> tryRead1 input+            if B.null rest+                then loop (acc . FQ2 x) 'b' rest+                else loop (acc . FQ2 x) 'B' $ B.tail rest+        'B' -> do +            input' <- tryRead1 input+            if B.head input' == '+'+                then loop acc 'c' $ B.tail input'+                else do+                    let (x, rest) = B.break (=='\n') input'+                    if B.null rest+                        then loop (acc . FQ2 x) 'b' rest+                        else loop (acc . FQ2 x) 'B' $ B.tail rest+        'c' -> do+            (x, rest) <- B.break (=='\n') <$> tryRead1 input+            if B.null rest+                then loop acc 'c' rest+                else loop acc 'd' $ B.tail rest+        'd' -> do+            (x, rest) <- B.break (=='\n') <$> tryRead1 input+            if B.null rest +                then loop (acc . FQ3 x) 'd' rest+                else loop (acc . FQ3 x) 'D' $ B.tail rest+        'D' -> if B.null input+            then await >>= \case+                Nothing -> yield $ fqBuilder $ acc Complete+                Just input' -> if B.head input' == '@'+                    then do+                        yield $ fqBuilder $ acc Complete+                        loop Init 'a' $ B.tail input'+                    else loop acc 'd' input'+            else if B.head input == '@'+                then do+                    yield $ fqBuilder $ acc Complete+                    loop Init 'a' $ B.tail input+                else loop acc 'd' input {-# INLINE parseFastqC #-} -fastqParser :: Parser Fastq-fastqParser = do-    _ <- skipWhile (/='@') >> char8 '@'-    ident <- A.takeTill isEndOfLine-    endOfLine-    sequ <- BS.filter (not . isEndOfLine) <$> takeTill (=='+')-    char8 '+' >> A.skipWhile (not . isEndOfLine) >> endOfLine-    score <- BS.filter (not . isEndOfLine) <$>-        A.scan 0 (f (B.length sequ))-    skipWhile (/='@')-    return $ Fastq ident sequ score+parseFastqC' :: MonadThrow m => ConduitT B.ByteString Fastq m ()+parseFastqC' = conduitParser fastqParser .| mapC snd   where-    f n i x | i >= n = Nothing-            | isEndOfLine x = Just i-            | otherwise = Just $ i + 1-{-# INLINE fastqParser #-}+    fastqParser = do+        _ <- skipWhile (/='@') >> char8 '@'+        ident <- A.takeTill isEndOfLine+        endOfLine+        sequ <- BS.filter (not . isEndOfLine) <$> takeTill (=='+')+        char8 '+' >> A.skipWhile (not . isEndOfLine) >> endOfLine+        score <- BS.filter (not . isEndOfLine) <$>+            A.scan 0 (f (B.length sequ))+        skipWhile (/='@')+        return $ Fastq ident sequ score+      where+        f n i x | i >= n = Nothing+                | isEndOfLine x = Just i+                | otherwise = Just $ i + 1+{-# INLINE parseFastqC' #-}  fastqToByteString :: Fastq -> B.ByteString-fastqToByteString (Fastq a b c) = "@" <> a <> "\n" <> b <> "\n+\n" <> c+fastqToByteString (Fastq a b c) = B.concat ["@", a, "\n", b, "\n+\n", c] {-# INLINE fastqToByteString #-}  -- | Get the mean and variance of quality scores at every position.@@ -87,7 +159,7 @@ meanVarianceC :: Monad m => ConduitT [Double] o m [(Double, Double)] meanVarianceC = peekC >>= \case     Nothing -> error "Empty input"-    Just x -> fst <$> foldlC f (replicate (length x) (0,0), 0)+    Just x -> fst <$> foldlC f (replicate (length x) (0,0), 0 :: Int)   where     f (acc, n) xs = let acc' = zipWith g acc xs in (acc', n')       where

@@ -21,8 +21,6 @@  type GOMap = M.HashMap GOId GO -type TermCount = M.HashMap GOId Int- -- | The top level is 0. getGOLevel :: GOId -> GOMap -> Int getGOLevel gid gm = loop 0 [gid]

@@ -29,12 +29,14 @@ import Data.Aeson import Data.Aeson.Types import Data.Aeson.Encode.Pretty (encodePretty)-import qualified Data.HashMap.Lazy as M+import qualified Data.Aeson.KeyMap as M+import qualified Data.Aeson.Key as M import qualified Data.ByteString.Lazy.Char8 as B import qualified Data.ByteString.Char8 as BS import qualified Data.Sequence as S import qualified Data.Text as T import qualified Data.Vector as V+import Data.Maybe (fromMaybe) import Network.HTTP.Conduit import Data.Default.Class @@ -115,7 +117,7 @@   (|@) :: Value -> T.Text -> Value-(|@) (Object obj) key = M.lookupDefault (error errMsg) key obj+(|@) (Object obj) key = fromMaybe (error errMsg) $ M.lookup (M.fromText key) obj   where     errMsg = "No such key: " ++ T.unpack key ++ " In: " ++ show obj (|@) _ _ = error "not an object"

@@ -7,7 +7,7 @@ import Data.Aeson import Data.List.Split (chunksOf) import qualified Data.ByteString.Char8 as B-import qualified Data.HashMap.Strict as M+import qualified Data.Aeson.KeyMap as M import Network.HTTP.Conduit  import Bio.RealWorld.ID (BioID(..), EnsemblID)

@@ -8,7 +8,7 @@     , filterFDR     , slideAverage     , hyperquick-    , kdeWeight+    , gaussianKDE     , kld     , jsd     , binarySearch@@ -95,19 +95,19 @@     e = 1e-20  -- | Assign weights to the points according to density estimation.-kdeWeight :: Int  -- ^ number of mesh points used in KDE-          -> U.Vector Double -> U.Vector Double-kdeWeight n xs = U.map getDensity xs+gaussianKDE :: Int  -- ^ number of mesh points used in KDE+            -> U.Vector Double -> (Double -> Double)+gaussianKDE n xs = \x -> +    let i = binarySearch points x+        lo = points U.! (i - 1)+        lo_d = den U.! (i - 1) +        hi = points U.! i+        hi_d = den U.! i+        hi_w = (x - lo) / (hi - lo)+        lo_w = 1 - hi_w+     in lo_w * lo_d + hi_w * hi_d   where     (points, den) = kde n xs-    getDensity x = let i = binarySearch points x-                       lo = points U.! (i - 1)-                       lo_d = den U.! (i - 1) -                       hi = points U.! i-                       hi_d = den U.! i-                       hi_w = (x - lo) / (hi - lo)-                       lo_w = 1 - hi_w-                    in lo_w * lo_d + hi_w * hi_d  -- | compute the Kullback-Leibler divergence between two valid (not check) probability distributions. -- kl(X,Y) = \sum_i P(x_i) log_2(P(x_i)\/P(y_i)).

@@ -3,6 +3,9 @@ module Tests.Fastq (tests) where  import           Bio.Data.Fastq+import Data.Conduit.Zlib (ungzip, multiple, gzip)+import qualified Data.ByteString.Char8 as B+import qualified Data.ByteString.Lazy.Char8 as BL import Lens.Micro import           Conduit import           Test.Tasty@@ -14,12 +17,19 @@  tests :: TestTree tests = testGroup "Test: Bio.Data.Fastq"-    [ fastqIO+    [ testCase "FASTQ IO" fastqIO     ] -fastqIO :: TestTree-fastqIO = goldenVsFile "FASTQ Read/Write Test" input output io-  where-    io = runResourceT $ runConduit $ streamFastq input .| sinkFastq output-    input = "tests/data/test.fastq" -    output = "out.fastq"+fastqIO :: Assertion+fastqIO = do+    a <- fmap B.concat $ runResourceT $ runConduit $+        sourceFile "tests/data/test.fastq.gz" .| multiple ungzip .| sinkList+    b <- fmap B.concat $ runResourceT $ runConduit $+        sourceFile "tests/data/test_wrap.fastq.gz" .| multiple ungzip .| sinkList+    let fq1 = B.concat $ replicate 1000 a+        fq2 = B.concat $ replicate 1000 b+        r1 = B.concat $ runIdentity $ runConduit $ yield fq1 .|+            parseFastqC .| mapC fastqToByteString .| unlinesAsciiC .| sinkList+        r2 = B.concat $ runIdentity $ runConduit $ yield fq2 .|+            parseFastqC .| mapC fastqToByteString .| unlinesAsciiC .| sinkList+    [True, True] @=? [r1 == fq1, r2 == fq1]

@@ -1,200 +0,0 @@-@M00436:256:000000000-B3PGP:1:1101:12997:1870 2:N:0:TAAGACGA-TTTTTCCCTCCTTTTCTCTTCTCCTCTTTTTTTTTTTTTTTTTTTTTTTTT-+-111>1111B1111313A33A1B11B01BDAB0AA/AAAAA>E>>>E>EE<<-@M00436:256:000000000-B3PGP:1:1101:20142:2157 2:N:0:TAAGGCGA-CATTAGAGCCTGTTATTAATGATTGTAATGTATTTTCTGTATAATTTTACT-+-11>>>13B1>>BBGFGBGGGGF3BBAGHFHHHHGG3FBFGHFHFGDFGFHG-@M00436:256:000000000-B3PGP:1:1101:15166:2177 2:N:0:TAAGGCGA-TGCCACGTGATTGCTGAGGCTGTAAGAACCACCCTGGGTCCCCGTGGCATG-+-A11>>1>>1>FFCGGFGGGGGGHHG3BDFGH0FGCCGGGGHGHGFCCGFHH-@M00436:256:000000000-B3PGP:1:1101:16584:2188 2:N:0:TAAGGCGA-CTAGTAAGGCATTGTAAAAGTTACTGGATTTGGTTTAAAAAAAAAAAAAA-+->A11>BF11>CBAA3BGGG11BEGAE1FD1GD1000EGGGHCGGGGG?E@-@M00436:256:000000000-B3PGP:1:1101:15256:2192 2:N:0:TAAGGCGA-CTTTGGAACAACTATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-+-1AA?11CFBFFABG3FGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-@M00436:256:000000000-B3PGP:1:1101:18301:2193 2:N:0:TAAGGCGA-CACCTACAGAAGGAGCGCTGTGCCCCCTGGAGCTGACAAGAAAGCTGAGGC-+-111>AFCC1DFFA1FG?FGAEGHHHGGGGABGGHHDG11000BFGHG1BFG-@M00436:256:000000000-B3PGP:1:1101:13721:2196 2:N:0:TAAGGCGA-TAGCCTGAGCGTTTAATTTATTCAGTACCTGTGTTTGTGTGAATGCGGTGT-+-111>AFFBBFDAECG3FGDGGGHGGHFHBGHHHBBFFGFGFHBGHGGGEAA-@M00436:256:000000000-B3PGP:1:1101:14584:2200 2:N:0:TAAGGCGA-GCAAAAGGACCATTTAAAGTAAAAAAAAAAAAAAAAAAAAAAAATCTCTCC-+-1>>1>BCAFFAAGFGG3FGG3FG3GG?ECGGGGGC?EGCEGGE@FH2B2BC-@M00436:256:000000000-B3PGP:1:1101:11335:2200 2:N:0:TAAGGCGA-CTGAATGCCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-+-1AAAA33@11113BGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-@M00436:256:000000000-B3PGP:1:1101:13303:2201 2:N:0:TAAGGCGA-TGCTTATACAATGTGAGTGTACTGAGGTAAGGGGAATATGGGAGCAGAGAC-+-A3>A?FFF5BCFFDGGGFGGGGHHGHGCF5GHA?EGGFGHGFFEEG3FHCG-@M00436:256:000000000-B3PGP:1:1101:13286:2203 2:N:0:TAAGGCGA-TTCCCGAGACCGGCAGGCCTCAGCCCAAAAGAACAAAGGGAGAAAGAACTG-+-1>111A>111>10AE00AA101110AGHH/0/00B0B00///A011B0011-@M00436:256:000000000-B3PGP:1:1101:11054:2203 2:N:0:TAAGGCGA-TTCGTACTCTGAGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGCACTC-+-1111>>1?DBF1BB31FFE3BA1B1E3BF1A0AEECAF////A/BA22BGC-@M00436:256:000000000-B3PGP:1:1101:15278:2204 2:N:0:TAAGGCGA-ACATAGTTCAGTATGAAAATAAGAGAATAAAATCTGTTATAAGCAAGTGAT-+-111>1@DFDBFFFGGGGF1BFGF1E11BDHFCGFDHGHHHH3GFH0GAEHH-@M00436:256:000000000-B3PGP:1:1101:14285:2204 2:N:0:TAAGGCGA-AATGTGCGTATTGAGCACATTAAGCACTCTAAGAGCCGAGATAGCTTCCTG-+-11>1AFBAAA1@D3GGGGGGGGG1GFFH0E1F31E0F?0AECBADDGGHHE-@M00436:256:000000000-B3PGP:1:1101:15307:2205 2:N:0:TAAGGCGA-TCTATAAGAAGGAGAAAGCTCGAGTCATCACTGAGGAAGAGAAGAATTTC-+-AA3AAFDDBDCFAGECGFFGGGGGHCFHHGHBGHHGHHHHHGHHHHHHBG-@M00436:256:000000000-B3PGP:1:1101:17837:2208 2:N:0:TAAGGCGA-GCAGAGGTGAATGGGATTCAGACGGTACTAAAAAAAAAAAAAAAAAAAAA-+-111>1A?1>FFFDCFGCEGGGGGCGEHEHFFHFFAEEGCEEGGGGGGGGG-@M00436:256:000000000-B3PGP:1:1101:14152:2208 2:N:0:TAAGGCGA-TCTATGCTCCCTCTGTGTTAGAATTGGCTGAAGTGTTTTTGTGCAGCTGAC-+-AA>A1BD311>1A113331BFGH3311010BFE313300000A1E1FE1F0-@M00436:256:000000000-B3PGP:1:1101:17005:2214 2:N:0:TAAGGCGA-GTCTTGAGAGCTTCCTTTTGCTTTCTTCTCTTGCCTCTGAGAACATCAGCC-+-1AAA>FFCA1A1B1EA3311B313A333313311B11B1F1FGCG1FH110-@M00436:256:000000000-B3PGP:1:1101:15244:2216 2:N:0:TAAGGCGA-GCCAAGAATGTGTTGTCTAAAATGCCTGTTTAGTTTTCAAGGATGGAACTC-+-1>>AAAFFD@333B11B3BGGGFAAEA11B3GEAD333FHB1F1EFHH11A-@M00436:256:000000000-B3PGP:1:1101:12952:2217 2:N:0:TAAGGCGA-GAACTGGAGCGTGTGGCCAAGTCTAACCGCTGATTTCCCAGCTGCTGCCT-+-111>AD1CFBDAEA11FFFGAAGFDFGF0EECE1GFHHFGFHHHFHHGFG-@M00436:256:000000000-B3PGP:1:1101:16915:2218 2:N:0:TAAGGCGA-ATGCACATGTGGTGTAGGAACTTTTTTCTACCATAAGTGACACCAATAAAT-+-3>3AAFFFFD@BAFFDFGGGGGHHHHGHGHCHGHHHBFBGGFGGGFHGHHH-@M00436:256:000000000-B3PGP:1:1101:11613:2220 2:N:0:TAAGGCGA-TGTGTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGATCTC-+-33>AADFFFFFFCGGGGFGGFCHHH4GFHFGDGGGCFFDGGEE1BFFHFH5-@M00436:256:000000000-B3PGP:1:1101:18615:2225 2:N:0:TAAGGCGA-CCTATCAGGAGTTCACTGACCACCTCGTCAAGACCCACACCAGAGTCTCCG-+->AAAAFFFFFB4FFGGFFGGGGHG4GDHGHGBGHBGHGGGGHGFEDGHHHG-@M00436:256:000000000-B3PGP:1:1101:11230:2227 2:N:0:TAAGGCGA-GTACTGTCACTTAACCCCTATTAACATACGGTGTTCAAGCCTTCCAGTATC-+-?A?AAFFFBDFBFDFFGCGGGGCFHFBDHFG4FE2DFFGHDGBGFGHBGBF-@M00436:256:000000000-B3PGP:1:1101:14569:2228 2:N:0:TAAGGCGA-GTGAATGGAAATGCCCCAACTAAATACTACCGTATGGCCCACCATAATTAC-+-3>AAAFFFBFFFGFGGFEFFGBGHGFHHHHHGGGGFGHHHGGGDH3GGHGH-@M00436:256:000000000-B3PGP:1:1101:15926:2228 2:N:0:TAAGGCGA-AATCTAGGAAAATAAAACAAGAGAAGCTGAATTAAAAAAAAAAAAAAAAA-+->AAA1FF1BDFFGGGGGFGG111B101ABGHDGGHHHHGGGGGGGGGGGG-@M00436:256:000000000-B3PGP:1:1101:15169:2228 2:N:0:TAAGGCGA-GTATCAACGAAAAGTGAGACTCATTGCTGCCCGCCGAAATGAACGGCTGCG-+-1>A1AFF1>1>AGB11313A11B3331311000A00/A//11B10//////-@M00436:256:000000000-B3PGP:1:1101:15774:2230 2:N:0:TAAGGCGA-CCCAAAGACAAGGAAAGGAAAAAATAAAAACAACAAATACCTAAAAGCTG-+-111>AFF11>C11111111BE0F0011D110000BGC1F1111BGGD011-@M00436:256:000000000-B3PGP:1:1101:11431:2230 2:N:0:TAAGGCGA-GAGCTGAACCTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-+-111>A1DD1>>1BGGDGGGCEEEEGGGCGGGGGGCEGCEEGCGCGCCCCG-@M00436:256:000000000-B3PGP:1:1101:19030:2230 2:N:0:TAAGGCGA-ATCCCATTACTCTCTTTGTGGAGAAGGAACGAGATAAGGAAGTCAGTGATG-+-1AAAAFFFFBBD3FFAFF3BEGGHHH00FG?EGGGGFFFHHG1FGHDGGHB-@M00436:256:000000000-B3PGP:1:1101:16869:2231 2:N:0:TAAGGCGA-CCTTCCACCTGGTCCGGAGATCCCTGGACCTTAGGAGGCACTCATTTTTCC-+-AAAA1>@D111111A1110A01101100A001BA110A/BC0AG12AA10A-@M00436:256:000000000-B3PGP:1:1101:12374:2231 2:N:0:TAAGGCGA-CTTTAGATGGTGGGGACATCATCAATGCCTTGTGCTTCAGCCCCAACCGCT-+-?AAAAFFFFBBDEEGGEGGGFGHHHG5FGGGHFEDGHHHHGHGGGEGG?EA-@M00436:256:000000000-B3PGP:1:1101:14609:2232 2:N:0:TAAGGCGA-TCCTCCTAAGTAACTGGGACTACATATGTGCATCACCACGTCCAGTTAATT-+-3>>AAFFFFFFFFGGGFAAG4GG4FD5A66DGHBHH4DC22BFE3GH5EFG-@M00436:256:000000000-B3PGP:1:1101:11898:2233 2:N:0:TAAGGCGA-GTACTGTAGTCACTCAGTATTTGTATATGTTGCTAGAATTTAGATTGTAA-+-1A1AAFFFFFFFGBGGGBEF3BF3FFGFFGGGHFBGGFFDGGFFFFHFGF-@M00436:256:000000000-B3PGP:1:1101:15215:2233 2:N:0:TAAGGCGA-GTAAAAGAGTATATGTAAACTGAATGAGAACTAAAAAATAGAAATAAAAC-+-AA1AAFF113@33333BFF1311B3311DF11FGGHH00B11DG1FAGH1-@M00436:256:000000000-B3PGP:1:1101:18320:2233 2:N:0:TAAGGCGA-GCATTTAATATTGATACACTTTCACCTCTAAAATGGATTTGAAGAAATGC-+-111>>DF3BBDFGGGGGG1FBGFFCHHHHGF3ADF1GGHFH2A1AB0BFG-@M00436:256:000000000-B3PGP:1:1101:13822:2234 2:N:0:TAAGGCGA-TCCACAAGTACTCTGGCAAGGAAGGAGACAAGCACACCCTGAGCAAGAAGG-+-BA3ABFA?DFFFFDGGCGGGCGHFE4AGFHBCGFHGFE2EFFFBHHEHBEF-@M00436:256:000000000-B3PGP:1:1101:12165:2235 2:N:0:TAAGGCGA-ACCATGCTGTGTCTGTTATGCGGCAAAGCCGAAGATACTAACAGTATTCTC-+-AA?A@1B11313A3133B311110AEH0000AE0E1F11F21B11D2222A-@M00436:256:000000000-B3PGP:1:1101:19900:2236 2:N:0:TAAGGCGA-CCATTTTAGTTCAGGAGTGTTTCCTTATTTTCTCTTTTCTGATAGAGTTT-+->>3>AFFFFFFFGGGGCGGABGHHHCFHHGGHHHHHHHHHHHHHGHFHHH-@M00436:256:000000000-B3PGP:1:1101:11136:2236 2:N:0:TAAGGCGA-GGAGAGGAGCGAGGCTGAGAGAAGAGAAGAACAATGTACTCATAAAGAAAC-+->111111B111110000A0B1AE0F0F101B00B112D2211112111B00-@M00436:256:000000000-B3PGP:1:1101:15661:2236 2:N:0:TAAGGCGA-GTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGCGATCCTCCCACCT-+->A>AABFFFFAAGGGFAFFFFGDEGECGF4FDFHFHHHGGEEEHGGG2FEG-@M00436:256:000000000-B3PGP:1:1101:20014:2238 2:N:0:TAAGGCGA-TGTGCATCACAGAGGTGTGCATCACCTTTGACCAGGCTGACCTGACCATC-+-1111>B3311DDGCC1A1ABGFFHHB1BAGHHHHFEC0FF001FGBHFHH-@M00436:256:000000000-B3PGP:1:1101:13789:2238 2:N:0:TAAGGCGA-ACCCTGGACTCTGGACTTCGCAGGTTCCTGCCTGTCACGCCACCCCCTTCC-+->A1A11AFFFBF31FGGCGGGGGGCFFHGBGHGHHHHHGHGGGHGGEEGFH-@M00436:256:000000000-B3PGP:1:1101:11741:2240 2:N:0:TAAGGCGA-CTCCATCCGGCACCCTGACGTTGAGGTGGATGGGTTCTCTGAGCTTCGGTG-+-1>1A1FDF11DDEECGGFG?FCGHC0B0AFEGCCGCAGBFGGGGGGFGGFE-@M00436:256:000000000-B3PGP:1:1101:19980:2240 2:N:0:TAAGGCGA-GATGTGCGCATTGACACCAGGCTCAACAAAGCTGTCTGGGCCAAAGGAAT-+-11>1>DBA@AAAGGFFGFGFGGCGHHHHG0FGFHGGHF00/GE/GFFFFH-@M00436:256:000000000-B3PGP:1:1101:20675:2240 2:N:0:TAAGGCGA-GGGTCCCTCTGTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGT-+-333AAAFFFFFFGGGGGGCFFGGFGHFHHHHHHHGHHGGGGEFGGGGGEGE-@M00436:256:000000000-B3PGP:1:1101:14624:2241 2:N:0:TAAGGCGA-TACTTATAAGTCTATCATTTAAAGACATGTACTGAAACAAATGTATTTGTT-+-A1>AAFFFBDDBG3EFGGGGB3FBGHHHFHHHHHFFGFB0BFGEBGGHHGH-@M00436:256:000000000-B3PGP:1:1101:11465:2241 2:N:0:TAAGGCGA-GCCTCACCGGTGACCAGCCTGGACTCGCATGGCAGCACCCAGGGCATGCTG-+-333AACAFAD>DGGGGGFGGGGHHGHGGEGCHFBEGCHHGGHGG1FGFHHG-@M00436:256:000000000-B3PGP:1:1101:20263:2242 2:N:0:TAAGGCGA-GTGTGAATGGGTTTATACTGATTTTGATATCATGTTCTTTTCATAGTCGT-+-111>ADDFFC?CCFGGGGGFFGFHHHGHHHCHHHHFHCHHHGHHHHHGFG-@M00436:256:000000000-B3PGP:1:1101:16263:2243 2:N:0:TAAGGCGA-GAACTATACTGACGAAGCCATTGAAACAGATGATCTGACCATTAAGCTGGT-+-11>AAFFFFFDFGGGG?GGGGGGGFHHHHHGHHBGHGFBFGGFHGFHFF00

binary file changed (absent → 2986 bytes)

binary file changed (absent → 3065 bytes)