From 5dffdecd5112d6c60c6ff285a8dd871086b7bc30 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 16 Aug 2023 16:38:39 +1000
Subject: remove lazy bytestrings

---
 Data/FastQ.hs | 34 ++++++++++++++--------------------
 dedumi.hs     |  6 ++++--
 2 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/Data/FastQ.hs b/Data/FastQ.hs
index 1f4f814..3e2f26c 100644
--- a/Data/FastQ.hs
+++ b/Data/FastQ.hs
@@ -21,6 +21,7 @@ import Data.Word (Word8)
 import Lens.Micro
 import Lens.Micro.TH
 import Streamly.Data.Array (Array)
+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
@@ -80,6 +81,7 @@ parse l r =
     parseEntry l r =
       let [hdr, seq, "+", qual] = SB.fromArray l & BC.lines
           [hdr', seq', "+", qual'] = SB.fromArray r & BC.lines
+          str = error $ "parseEntry:" <> BC.unpack str
        in (Read qual seq hdr, Read qual' seq' hdr')
 
 unparse :: FilePath -> FilePath -> Stream IO ReadPair -> IO ()
@@ -88,39 +90,31 @@ unparse l r str = do
   rh <- openFile r WriteMode
   ld <- initDeflate 0 gzipWindow
   rd <- initDeflate 0 gzipWindow
-  fmap unparse' str & toLazyBS >>= uncurry (writeFiles lh rh ld rd)
+  fmap unparse' str & S.fold (F.drainMapM $ writeFiles lh rh ld rd)
+  flush rd rh
+  flush ld lh
+  hClose rh
+  hClose lh
   where
-    writeFiles l r ld rd (BSL.Chunk a as) (BSL.Chunk b bs) = do
+    writeFiles l r ld rd (a, b) = do
       putCompressed ld l a
       putCompressed rd r b
-      writeFiles l r ld rd as bs
-    writeFiles l r ld rd BSL.Empty BSL.Empty = do
-      flush rd r
-      flush ld l
-    writeFiles _ _ _ _ _ _ = error "unparse: stream mismatch"
 
     putCompressed d h chunk = do
       popper <- feedDeflate d chunk
-      writePopper popper h
+      writePopper h popper
 
-    flush d h =
-      finishDeflate d >>= \case
-        Just rest -> B.hPut h rest
-        Nothing -> pure ()
+    flush d h = finishDeflate d & writePopper h
 
-    writePopper p h =
+    writePopper h p =
       p >>= \case
         Just str -> do
           B.hPut h str
-          writePopper p h
+          writePopper h p
         Nothing -> pure ()
 
     unparse' :: ReadPair -> (ByteString, ByteString)
     unparse' read =
-      ( BC.unlines [read ^. _1 . header, read ^. _1 . nucs, "+", read ^. _1 . qual],
-        BC.unlines [read ^. _2 . header, read ^. _2 . nucs, "+", read ^. _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)
-    toLazyBS =
-      S.foldrM (\(l, r) b -> bimap (BSL.chunk ("@" <> l)) (BSL.chunk ("@" <> r)) <$> unsafeInterleaveIO b) (pure (BSL.Empty, BSL.Empty))
diff --git a/dedumi.hs b/dedumi.hs
index aa682f1..4215026 100644
--- a/dedumi.hs
+++ b/dedumi.hs
@@ -15,6 +15,7 @@ import Data.Function
 import GHC.Prim (RealWorld)
 import GHC.TypeLits
 import Lens.Micro
+import qualified Streamly.Data.Fold as F
 import qualified Streamly.Data.Stream as S
 import System.Environment
 
@@ -42,10 +43,10 @@ insert' :: (KnownNat b, KnownNat f) => CuckooFilter RealWorld b f ByteString ->
 insert' f x =
   let y = B.take (umiLength + extraHashBases) (x ^. _1 . nucs) <> B.take (umiLength + extraHashBases) (x ^. _2 . nucs)
    in member f y >>= \case
-        True -> pure True
+        True -> pure False
         False ->
           insert f y >>= \case
-            True -> pure False
+            True -> pure True
             False -> error "filter full"
 
 main :: IO ()
@@ -57,4 +58,5 @@ main = do
   parse p1 p2
     & S.filterM (insert' f)
     & fmap trim
+    -- & S.fold (F.drainMapM print)
     & unparse p3 p4
-- 
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