Refactoring code to reduce duplication

Author: recursion-ninja

app/generate-timings/Main.hs

@@ -298,12 +298,8 @@ generateTruncatedDataFile taxaNumPadder strLenPadder filePath counter taxaSize (
             , taxaFilePath
             ]
 
-    _ <- deleteFileIfExists taxaFilePath
-    _ <- deleteFileIfExists lessFilePath
+    p <- makeCleanProcess counter [taxaFilePath, lessFilePath] commandStr
 
-    let p = makeProcessFromCommand commandStr
-
-    printCounter counter
     putStrLn $ unwords [ taxaNumPadder taxaSize, strLenPadder strLength ]
 
     (_exitCode, stdOut, _stdErr) <- readCreateProcessWithExitCode p ""
@@ -339,11 +335,8 @@ generateTruncatedTreeFile taxaNumPadder filePath counter (taxaSize, taxaFilePath
             , taxaFilePath <.> "deleted"
             ]
 
-    _ <- deleteFileIfExists lessFilePath
+    p <- makeCleanProcess counter [lessFilePath] commandStr
 
-    let p = makeProcessFromCommand commandStr
-
-    printCounter counter
     putStrLn $ taxaNumPadder taxaSize
 
     (_exitCode, stdOut, _stdErr) <- readCreateProcessWithExitCode p ""
@@ -388,9 +381,8 @@ timeFilePoint taxaNumPadder strLenPadder counter tcmPath fp = do
             , "/dev/null"
             ]
 
-    let p = makeProcessFromCommand commandStr
+    p <- makeCleanProcess counter [] commandStr
 
-    printCounter counter
 --    putStrLn $ fileDataPath fp
     putStrLn $ unwords [ taxaNumPadder $ taxaCount fp
                        ,  strLenPadder $ stringLength fp
@@ -402,6 +394,14 @@ timeFilePoint taxaNumPadder strLenPadder counter tcmPath fp = do
     pure $ force (taxaCount fp, stringLength fp, postOrder, preOrder)
 
 
+makeCleanProcess :: IORef (Word, Word) -> [FilePath] -> String -> IO CreateProcess
+makeCleanProcess counter files commandStr = do
+    traverse_ deleteFileIfExists files
+    let p = makeProcessFromCommand commandStr
+    printCounter counter
+    pure p
+
+
 makeProcessFromCommand :: String -> CreateProcess
 makeProcessFromCommand commandStr =
     CreateProcess

efficient-implied-alignment.cabal

@@ -107,6 +107,7 @@ library
     , mtl
     , parser-combinators >=1.2
     , pointed
+    , primitive          >=0.7
     , QuickCheck
     , scientific
     , semigroupoids

src/Alignment/Pairwise/Internal.hs

@@ -19,7 +19,6 @@
 {-# LANGUAGE FlexibleContexts      #-}
 {-# LANGUAGE FlexibleInstances     #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
-{-# LANGUAGE TypeSynonymInstances  #-}
 {-# LANGUAGE TypeFamilies          #-}
 
 -- To add Indexable/Lookup instances for Matrix
@@ -424,23 +423,23 @@ deleteGaps gap bvs
             gapLen  <- newSTRef 0
             gapRefs <- newSTRef []
 
+            let handleGapBefore op = do
+                    gapBefore <- readSTRef prevGap
+                    when gapBefore $ do
+                      j <- readSTRef nonGaps
+                      g <- readSTRef gapLen
+                      modifySTRef gapRefs ( (j,g): )
+                      op
+
             for_ [0 .. charLen - 1] $ \i ->
               if symbolAlignmentMedian (bvs ! i)  == gap
               then modifySTRef gapLen succ *> writeSTRef prevGap True
-              else do gapBefore <- readSTRef prevGap
-                      when gapBefore $ do
-                        j <- readSTRef nonGaps
-                        g <- readSTRef gapLen
-                        modifySTRef gapRefs ( (j,g): )
+              else do handleGapBefore $ do
                         writeSTRef  gapLen 0
                         writeSTRef prevGap False
                       modifySTRef nonGaps succ
-            
-            gapBefore <- readSTRef prevGap
-            when gapBefore $ do
-              j <- readSTRef nonGaps
-              g <- readSTRef gapLen
-              modifySTRef gapRefs ( (j,g): )
+
+            handleGapBefore $ pure ()
             readSTRef gapRefs