tidy, more fusion, handle different read headers

3 files changed, 18 insertions, 20 deletions

diff --git a/Data/FastQ.hs b/Data/FastQ.hs
index 5f33d27..217d58a 100644
--- a/Data/FastQ.hs
+++ b/Data/FastQ.hs
@@ -32,23 +32,18 @@ import Streamly.Internal.Data.Unfold.Type (Unfold (..))
 import qualified Streamly.Internal.FileSystem.File as File
 import System.IO
 import System.IO.Unsafe (unsafeInterleaveIO)
-import Prelude hiding (Read, reads)
+import Prelude hiding (Read)
 
 data Read = Read
   { _qual :: ByteString,
-    _nucs :: ByteString
+    _nucs :: ByteString,
+    _header :: ByteString
   }
   deriving (Eq, Show, Ord)
 
 makeLenses ''Read
 
-data ReadPair = ReadPair
-  { _header :: ByteString,
-    _reads :: (Read, Read)
-  }
-  deriving (Eq, Show, Ord)
-
-makeLenses ''ReadPair
+type ReadPair = (Read, Read)
 
 parse :: MonadIO m => FilePath -> FilePath -> Stream m ReadPair
 parse l r =
@@ -66,8 +61,8 @@ parse l r =
 
     parseEntry l r =
       let [hdr, seq, "+", qual] = SB.fromArray l & BC.lines
-          [_, seq', "+", qual'] = SB.fromArray r & BC.lines
-       in ReadPair hdr (Read qual seq, Read qual' seq')
+          [hdr', seq', "+", qual'] = SB.fromArray r & BC.lines
+       in (Read qual seq hdr, Read qual' seq' hdr')
 
 unparse :: FilePath -> FilePath -> Stream IO ReadPair -> IO ()
 unparse l r str = do
@@ -83,9 +78,10 @@ unparse l r str = do
     writeFiles l _ a BSL.Empty = BSL.hPut l a
     writeFiles _ r BSL.Empty b = BSL.hPut r b
 
+    unparse' :: ReadPair -> (ByteString, ByteString)
     unparse' read =
-      ( BC.unlines [read ^. header, read ^. reads . _1 . nucs, "+", read ^. reads . _1 . qual],
-        BC.unlines [read ^. header, read ^. reads . _2 . nucs, "+", read ^. reads . _2 . qual]
+      ( BC.unlines [read ^. _1 . header, read ^. _1 . nucs, "+", read ^. _1 . qual],
+        BC.unlines [read ^. _2 . header, read ^. _2 . nucs, "+", read ^. _2 . qual]
       )
 
     toLazyBS :: Stream IO (ByteString, ByteString) -> IO (BSL.ByteString, BSL.ByteString)
diff --git a/dedumi.hs b/dedumi.hs
index 01d9b37..7bf6dd4 100644
--- a/dedumi.hs
+++ b/dedumi.hs
@@ -15,7 +15,6 @@ import Data.Typeable
 import Lens.Micro
 import qualified Streamly.Data.Stream as S
 import System.Environment
-import Prelude hiding (reads)
 
 instance CuckooFilterHash ByteString where
   cuckooHash (Salt s) = saltedFnv1aByteString s
@@ -27,13 +26,13 @@ umiLength = 8
 
 trim x =
   x
-    & reads . _1 . nucs %~ B.drop umiLength
-    & reads . _2 . nucs %~ B.drop umiLength
-    & reads . _1 . qual %~ B.drop umiLength
-    & reads . _2 . qual %~ B.drop umiLength
+    & _1 . nucs %~ B.drop umiLength
+    & _2 . nucs %~ B.drop umiLength
+    & _1 . qual %~ B.drop umiLength
+    & _2 . qual %~ B.drop umiLength
 
 insert' f x =
-  let y = B.take umiLength (x ^. reads . _1 . nucs) <> B.take umiLength (x ^. reads . _2 . nucs)
+  let y = B.take umiLength (x ^. _1 . nucs) <> B.take umiLength (x ^. _2 . nucs)
    in member f y >>= \case
         True -> pure True
         False ->
diff --git a/package.yaml b/package.yaml
index a923f2d..4996d83 100644
--- a/package.yaml
+++ b/package.yaml
@@ -2,6 +2,7 @@ name: dedumi
 
 dependencies:
   - base
+  - fusion-plugin
   - zlib
   - cuckoo
   - microlens-th
@@ -15,4 +16,6 @@ dependencies:
 executables:
   dedumi:
     main: dedumi.hs
-    ghc-options: [-O2, -fspec-constr-recursive=10, -fmax-worker-args=16]
+    ghc-options: [-O2, -fspec-constr-recursive=10, -fmax-worker-args=16, -fplugin=Fusion.Plugin]
+    other-modules:
+      - Data.FastQ