diff --git a/src/GEval/Core.hs b/src/GEval/Core.hs
index f7e8b04..e5ff9b1 100644
--- a/src/GEval/Core.hs
+++ b/src/GEval/Core.hs
@@ -40,6 +40,7 @@ module GEval.Core
       checkMultipleOuts,
       checkMultipleOutsCore,
       gesMainMetric,
+      gesMainScheme,
       gesPreprocess,
       getDataDecoder,
       threeLineSource,
@@ -177,6 +178,11 @@ gesMainMetric spec = case gesMetrics spec of
   (scheme:_) -> evaluationSchemeMetric scheme
   otherwise -> error "no metric given"
 
+gesMainScheme :: GEvalSpecification -> EvaluationScheme
+gesMainScheme spec = case gesMetrics spec of
+  (scheme:_) -> scheme
+  otherwise -> error "no metric given"
+
 gesPreprocess :: GEvalSpecification -> (Text -> Text)
 gesPreprocess spec = tokenizeTabSeparatedWithSpaces (gesTokenizer spec)
 
diff --git a/src/GEval/LineByLine.hs b/src/GEval/LineByLine.hs
index 41c9283..549de1e 100644
--- a/src/GEval/LineByLine.hs
+++ b/src/GEval/LineByLine.hs
@@ -23,6 +23,7 @@ module GEval.LineByLine
 
 import GEval.Core
 import GEval.Common
+import GEval.EvaluationScheme
 import Text.Tokenizer
 
 import Data.Conduit.AutoDecompress (doNothing)
@@ -359,8 +360,9 @@ runLineByLineGeneralized ordering spec consum = do
   (inputFilePath, expectedFilePath, outFilePath) <- checkAndGetFilesSingleOut True spec
   gevalLineByLineCore metric mSelector preprocess inputFilePath expectedFilePath outFilePath (sorter ordering .| consum mReferences)
   where metric = gesMainMetric spec
+        scheme = gesMainScheme spec
         mSelector = gesSelector spec
-        preprocess = gesPreprocess spec
+        preprocess = (gesPreprocess spec) . (applyPreprocessingOperations scheme)
         sorter KeepTheOriginalOrder = doNothing
         sorter ordering = gobbleAndDo $ sortBy (sortOrder ordering (getMetricOrdering metric))
         sortOrder FirstTheWorst TheHigherTheBetter = compareScores
@@ -414,7 +416,8 @@ runMultiOutputGeneralized spec consum = do
   runResourceT $ runConduit $
     (sequenceSources sources .| consum)
   where metric = gesMainMetric spec
-        preprocess = gesPreprocess spec
+        scheme = gesMainScheme spec
+        preprocess = (gesPreprocess spec) . (applyPreprocessingOperations scheme)
         mSelector = gesSelector spec
 
 runMostWorseningFeatures :: ResultOrdering -> FilePath -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()