From d814e4da1720f01725caa1e82a1ffff7a675720d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 19 Mar 2024 16:03:38 +1100
Subject: fix sloppy fastq parsing

Previously chunked on @, which prevented it being used in
quality scores
---
 Data/FastQ.hs | 30 ++++++++++++++++++++----------
 package.yaml  |  1 +
 test.hs       | 21 +++++++++++++--------
 3 files changed, 34 insertions(+), 18 deletions(-)

diff --git a/Data/FastQ.hs b/Data/FastQ.hs
index 940c875..cdf8d7c 100644
--- a/Data/FastQ.hs
+++ b/Data/FastQ.hs
@@ -1,5 +1,6 @@
 {-# LANGUAGE LambdaCase #-}
 {-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE PatternSynonyms #-}
 {-# LANGUAGE StrictData #-}
 {-# LANGUAGE TemplateHaskell #-}
 {-# LANGUAGE TupleSections #-}
@@ -9,6 +10,7 @@
 module Data.FastQ where
 
 import Control.Monad
+import Control.Applicative
 import Control.Monad.IO.Class (MonadIO, liftIO)
 import Data.ByteString (ByteString)
 import qualified Data.ByteString as B
@@ -24,7 +26,7 @@ import qualified Streamly.Data.Fold as F
 import Streamly.Data.Stream (Stream)
 import qualified Streamly.Data.Stream as S
 import qualified Streamly.External.ByteString as SB
-import Streamly.Internal.Data.Stream.Chunked as AS
+import qualified Streamly.Internal.Data.Stream.Chunked as AS
 import Streamly.Internal.Data.Stream.StreamD.Type (Step (..))
 import Streamly.Internal.Data.Unfold.Type (Unfold (..))
 import System.IO
@@ -44,14 +46,15 @@ type ReadPair = (Read, Read)
 gzipWindow :: WindowBits
 gzipWindow = WindowBits 31
 
-parse :: MonadIO m => FilePath -> FilePath -> Stream m ReadPair
+parse :: (MonadIO m) => FilePath -> FilePath -> Stream m ReadPair
 parse l r =
   S.zipWith
-    parseEntry
-    (S.unfold streamBGZFile l & AS.splitOn 64 & S.drop 1)
-    (S.unfold streamBGZFile r & AS.splitOn 64 & S.drop 1)
+    (liftA2 (,))
+    (S.unfold streamBGZFile l & AS.splitOn 10 & fmap SB.fromArray & S.foldMany parseRead)
+    (S.unfold streamBGZFile r & AS.splitOn 10 & fmap SB.fromArray & S.foldMany parseRead)
+    & S.catMaybes
   where
-    streamBGZFile :: MonadIO m => Unfold m FilePath (Array Word8)
+    streamBGZFile :: (MonadIO m) => Unfold m FilePath (Array Word8)
     streamBGZFile = Unfold step seed
       where
         seed path = liftIO $ do
@@ -88,10 +91,17 @@ parse l r =
             PRDone -> pure $ Yield (SB.toArray "") (Just (h, i, Nothing))
             PRError e -> error $ "parse:" <> show e
 
-    parseEntry l r =
-      case (SB.fromArray l & BC.lines, SB.fromArray r & BC.lines) of
-        ([hdr, seq, "+", qual], [hdr', seq', "+", qual']) -> (Read qual seq hdr, Read qual' seq' hdr')
-        e -> error $ "parseEntry:" <> show e
+    parseRead =
+      (liftA4 (\(64 :. hdr) seq "+" qual -> Read qual seq hdr))
+        <$> F.one
+        <*> F.one
+        <*> F.one
+        <*> F.one
+
+    liftA4 fn a b c d = fn <$> a <*> b <*> c <*> d
+
+pattern (:.) :: Word8 -> ByteString -> ByteString
+pattern a :. b <- (B.uncons -> Just (a, b))
 
 unparse :: FilePath -> FilePath -> Stream IO ReadPair -> IO ()
 unparse l r str = do
diff --git a/package.yaml b/package.yaml
index 033ece3..515b9ff 100644
--- a/package.yaml
+++ b/package.yaml
@@ -25,5 +25,6 @@ tests:
     main: test.hs
     dependencies:
       - QuickCheck
+      - temporary
     other-modules:
       - Data.FastQ
diff --git a/test.hs b/test.hs
index a8780ff..b0574a1 100644
--- a/test.hs
+++ b/test.hs
@@ -10,6 +10,7 @@ import Data.Function
 import qualified Streamly.Data.Fold as F
 import qualified Streamly.Data.Stream as S
 import qualified Streamly.Data.Unfold as U
+import System.IO.Temp
 import Test.QuickCheck
 import Test.QuickCheck.Arbitrary
 import Test.QuickCheck.Monadic
@@ -19,15 +20,19 @@ instance Arbitrary Read where
   arbitrary = Read <$> genStr <*> genStr <*> genStr
     where
       genBS = fmap B.pack . listOf . elements
-      genStr = genBS $ [' ' .. '*'] ++ [',' .. '?'] ++ ['A' .. '~']
+      genStr = genBS $ [' ' .. '~']
 
 main :: IO ()
 main = quickCheckWith stdArgs {maxSuccess = 10000} $ \rp -> monadicIO $ do
-  rp' <- run $ do
-    S.unfold U.fromList rp & unparse "a" "b"
-    cnt <- B.readFile "a"
-    B.writeFile "a" $ cnt <> cnt
-    cnt <- B.readFile "b"
-    B.writeFile "b" $ cnt <> cnt
-    parse "a" "b" & S.fold F.toList
+  rp' <- run $ withSystemTempDirectory "dedumi-test" $ \root -> do
+    let a = root <> "/a"
+        b = root <> "/b"
+        a' = root <> "/a2"
+        b' = root <> "/b2"
+    S.unfold U.fromList rp & unparse a b
+    cnt <- B.readFile a
+    B.writeFile a' $ cnt <> cnt
+    cnt <- B.readFile b
+    B.writeFile b' $ cnt <> cnt
+    parse a' b' & S.fold F.toList
   assert $ rp <> rp == rp'
-- 
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