RFCT Replace unnecessary uses of missingH utils

NGLess/FileManagement.hs

@@ -42,7 +42,7 @@ import           System.FilePath (takeBaseName, takeDirectory, (</>), (<.>), (-<
 import           Control.Monad (unless, forM_, when)
 import           System.Posix.Files (setFileMode)
 import           System.Posix.Internals (c_getpid)
-import           Data.String.Utils (endswith)
+import           Data.List (isSuffixOf)
 
 import System.Directory
 import System.IO
@@ -74,6 +74,8 @@ data Compression = NoCompression
                 | ZStdCompression
                 deriving (Eq)
 
+endswith = flip isSuffixOf
+
 inferCompression :: FilePath -> Compression
 inferCompression fp
     | endswith ".gz" fp = GzipCompression

NGLess/StandardModules/Mappers/Bwa.hs

@@ -1,4 +1,4 @@
-{- Copyright 2013-2019 NGLess Authors
+{- Copyright 2013-2020 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE RankNTypes #-}
@@ -11,7 +11,7 @@ module StandardModules.Mappers.Bwa
 
 import           System.Directory (doesFileExist)
 import           System.Posix (getFileStatus, fileSize, FileOffset)
-import           System.Path (splitExt)
+import           System.FilePath (splitExtension)
 import           Control.Monad.IO.Class (liftIO)
 import qualified Data.ByteString as B
 
@@ -32,7 +32,7 @@ import Utils.Process (runProcess)
 -- of bwa use different indices
 indexPrefix :: FilePath -> NGLessIO FilePath
 indexPrefix base = do
-    let (basename, ext) = splitExt base
+    let (basename, ext) = splitExtension base
     return $ basename ++ "-bwa-" ++ bwaVersion ++ ext
 
 -- | Checks whether all necessary files are present for a BWA index

NGLess/StandardModules/Mappers/Minimap2.hs

@@ -1,4 +1,4 @@
-{- Copyright 2018-2019 NGLess Authors
+{- Copyright 2018-2020 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE RankNTypes #-}
@@ -10,7 +10,7 @@ module StandardModules.Mappers.Minimap2
     ) where
 
 import           System.Directory (doesFileExist)
-import           System.Path (splitExt)
+import           System.FilePath (splitExtension)
 import           Control.Monad.IO.Class (liftIO)
 import qualified Data.Vector as V
 import qualified Data.ByteString as B
@@ -38,7 +38,7 @@ import FileManagement (makeNGLTempFile, minimap2Bin)
 
 indexName :: FilePath -> FilePath
 indexName fp = base ++ "-minimap2-" ++ minimap2Version ++ ext ++ ".mm2.idx"
-    where (base, ext) = splitExt fp
+    where (base, ext) = splitExtension fp
 
 hasValidIndex :: FilePath -> NGLessIO Bool
 hasValidIndex = liftIO . doesFileExist . indexName

NGLess/StandardModules/Mocat.hs

@@ -20,12 +20,12 @@ import           Control.Monad.Extra (unlessM)
 import           System.Directory (doesDirectoryExist)
 import System.FilePath
 import System.FilePath.Glob
-import Data.List.Utils
 import Control.Monad.IO.Class (liftIO)
 import Control.Monad
 import Data.Maybe
 import Data.Default
-import Data.List (sort, isInfixOf)
+import Data.List (sort, nub, isInfixOf, isSuffixOf)
+
 
 import Output
 import NGLess
@@ -35,6 +35,8 @@ import FileManagement
 import Utils.Conduit
 import Utils.Utils (dropEnd)
 
+endswith = flip isSuffixOf
+
 exts :: [FilePath]
 exts = do
     fq <- ["fq", "fastq"]
@@ -48,8 +50,8 @@ pairedEnds = do
     return (s1 ++ "." ++ end, s2 ++ "." ++ end)
 
 buildSingle m1
-    | "pair.1" `isInfixOf` m1 = replace "pair.1" "single" m1
-    | "pair.2" `isInfixOf` m1 = replace "pair.2" "single" m1
+    | "pair.1" `isInfixOf` m1 = T.unpack $ T.replace "pair.1" "single" (T.pack m1)
+    | "pair.2" `isInfixOf` m1 = T.unpack $ T.replace "pair.2" "single" (T.pack m1)
     | otherwise = "MARKER_FOR_FILE_WHICH_DOES_NOT_EXIST"
 
 mocatSamplePaired :: [FilePath] -> T.Text -> Bool -> NGLessIO [Expression]
@@ -60,8 +62,8 @@ mocatSamplePaired fqfiles encoding doQC = do
                         | (endswith p1 fp) -> Just (fp, dropEnd (length p1) fp ++ p2)
                         | (endswith p2 fp) -> Just (dropEnd (length p2) fp ++ p1, fp)
                         | otherwise -> Nothing
-        -- match1 returns repeated entries if both pair.1 and pair.2 exist, uniq removes duplicate records
-        matched1 = uniq $ mapMaybe match1 fqfiles
+        -- match1 returns repeated entries if both pair.1 and pair.2 exist, `nub` removes duplicate records
+        matched1 = nub $ mapMaybe match1 fqfiles
         encodeStr = ConstStr . T.pack
     (exps,used) <- fmap unzip $ forM matched1 $ \(m1,m2) -> do
         let singles = buildSingle m1

NGLess/Validation.hs

@@ -15,8 +15,7 @@ import           Control.Monad.Extra (whenJust)
 import           Control.Monad.Writer.Strict
 import           Control.Monad.RWS
 import           Control.Monad (foldM_)
-import           Data.String.Utils (endswith)
-import           Data.List (find)
+import           Data.List (find, isSuffixOf)
 import           Data.Maybe
 import           Data.Char (isUpper)
 import           Data.Foldable (asum)
@@ -27,6 +26,9 @@ import NGLess.NGError
 import BuiltinFunctions
 import Utils.Suggestion
 
+
+endswith = flip isSuffixOf
+
 findMethod :: MethodName -> Maybe MethodInfo
 findMethod m = find ((==m) . methodName) builtinMethods