From e17f009dc5f1750f47f4ef950b2032b4bd283e67 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 18 Aug 2023 11:31:44 +1000
Subject: add tests and bugfix for small BGZip files

---
 Data/FastQ.hs | 38 +++++++++++++++++++++-----------------
 dedumi.hs     |  2 --
 package.yaml  |  8 ++++++++
 test.hs       | 33 +++++++++++++++++++++++++++++++++
 4 files changed, 62 insertions(+), 19 deletions(-)
 create mode 100644 test.hs

diff --git a/Data/FastQ.hs b/Data/FastQ.hs
index 158db3a..940c875 100644
--- a/Data/FastQ.hs
+++ b/Data/FastQ.hs
@@ -10,12 +10,10 @@ module Data.FastQ where
 
 import Control.Monad
 import Control.Monad.IO.Class (MonadIO, liftIO)
-import Data.Bifunctor (bimap)
 import Data.ByteString (ByteString)
 import qualified Data.ByteString as B
 import qualified Data.ByteString.Char8 as BC
-import qualified Data.ByteString.Lazy as BSL
-import qualified Data.ByteString.Lazy.Internal as BSL
+import Data.ByteString.Lazy.Internal (defaultChunkSize)
 import Data.Function
 import Data.Streaming.Zlib
 import Data.Word (Word8)
@@ -43,6 +41,7 @@ makeLenses ''Read
 
 type ReadPair = (Read, Read)
 
+gzipWindow :: WindowBits
 gzipWindow = WindowBits 31
 
 parse :: MonadIO m => FilePath -> FilePath -> Stream m ReadPair
@@ -61,22 +60,27 @@ parse l r =
           pure $ Just (h, i, Nothing)
         step Nothing = pure Stop
         step (Just (h, i, Nothing)) = liftIO $ do
-          chunk <- B.hGet h BSL.defaultChunkSize
-          if chunk == B.empty
+          complete <- isCompleteInflate i
+          (frag, unused, i) <-
+            if complete
+              then do
+                f <- finishInflate i
+                u <- getUnusedInflate i
+                (f,u,) <$> initInflate gzipWindow
+              else pure ("", "", i)
+          if unused == ""
             then do
-              hClose h
-              str <- finishInflate i
-              pure $ Yield (SB.toArray str) Nothing
+              chunk <- B.hGet h defaultChunkSize
+              if chunk == B.empty
+                then do
+                  hClose h
+                  str <- finishInflate i
+                  pure $ Yield (SB.toArray $ frag <> str) Nothing
+                else do
+                  popper <- feedInflate i $ chunk
+                  pure $ Yield (SB.toArray frag) (Just (h, i, Just popper))
             else do
-              complete <- isCompleteInflate i
-              (frag, unused, i) <-
-                if complete
-                  then do
-                    f <- finishInflate i
-                    u <- getUnusedInflate i
-                    (f,u,) <$> initInflate gzipWindow
-                  else pure ("", "", i)
-              popper <- feedInflate i $ unused <> chunk
+              popper <- feedInflate i $ unused
               pure $ Yield (SB.toArray frag) (Just (h, i, Just popper))
         step (Just (h, i, Just popper)) = liftIO $ do
           popper >>= \case
diff --git a/dedumi.hs b/dedumi.hs
index 4215026..5ca07a1 100644
--- a/dedumi.hs
+++ b/dedumi.hs
@@ -15,7 +15,6 @@ 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
 
@@ -58,5 +57,4 @@ main = do
   parse p1 p2
     & S.filterM (insert' f)
     & fmap trim
-    -- & S.fold (F.drainMapM print)
     & unparse p3 p4
diff --git a/package.yaml b/package.yaml
index bf95141..f0438a7 100644
--- a/package.yaml
+++ b/package.yaml
@@ -18,3 +18,11 @@ executables:
     ghc-options: [-O2, -fdicts-strict, -fspec-constr-recursive=16, -fmax-worker-args=16, -fplugin=Fusion.Plugin, -Wall, -Wno-name-shadowing]
     other-modules:
       - Data.FastQ
+
+tests:
+  tests:
+    main: test.hs
+    dependencies:
+      - QuickCheck
+    other-modules:
+      - Data.FastQ
diff --git a/test.hs b/test.hs
new file mode 100644
index 0000000..a8780ff
--- /dev/null
+++ b/test.hs
@@ -0,0 +1,33 @@
+{-# LANGUAGE DataKinds #-}
+{-# LANGUAGE QuasiQuotes #-}
+{-# LANGUAGE ScopedTypeVariables #-}
+
+module Main where
+
+import qualified Data.ByteString.Char8 as B
+import Data.FastQ
+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 Test.QuickCheck
+import Test.QuickCheck.Arbitrary
+import Test.QuickCheck.Monadic
+import Prelude hiding (Read)
+
+instance Arbitrary Read where
+  arbitrary = Read <$> genStr <*> genStr <*> genStr
+    where
+      genBS = fmap B.pack . listOf . elements
+      genStr = genBS $ [' ' .. '*'] ++ [',' .. '?'] ++ ['A' .. '~']
+
+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
+  assert $ rp <> rp == rp'
-- 
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