diff --git a/jplag/src/main/java/de/jplag/JPlag.java b/jplag/src/main/java/de/jplag/JPlag.java
index 0d3fb6c84..ed3806ec9 100644
--- a/jplag/src/main/java/de/jplag/JPlag.java
+++ b/jplag/src/main/java/de/jplag/JPlag.java
@@ -302,7 +302,7 @@ private void parseBaseCodeSubmission(Submission subm) throws ExitException {
         long startTime = System.currentTimeMillis();
         print("----- Parsing basecode submission: " + subm.getName() + "\n", null);
 
-        switch (subm.parse(options.getMinimumTokenMatch())) {
+        switch (subm.parse(options.isDebugParser(), options.getMinimumTokenMatch())) {
         case OK:
             break;
 
@@ -353,7 +353,7 @@ private void parseSubmissions(List<Submission> submissions) throws ExitException
             count++;
 
             // Parse the submission and process the results.
-            switch (subm.parse(options.getMinimumTokenMatch())) {
+            switch (subm.parse(options.isDebugParser(), options.getMinimumTokenMatch())) {
             case OK:
                 break;
 
diff --git a/jplag/src/main/java/de/jplag/Submission.java b/jplag/src/main/java/de/jplag/Submission.java
index 7f4eea984..09ab41ba4 100644
--- a/jplag/src/main/java/de/jplag/Submission.java
+++ b/jplag/src/main/java/de/jplag/Submission.java
@@ -121,7 +121,7 @@ public void setState(SubmissionState newState) {
      * Parse the submission.
      * @return State of the submission after the parse.
      */
-    public SubmissionState parse(int minimumTokenLength) {
+    public SubmissionState parse(boolean storeFilesWithParseErrors, int minimumTokenLength) {
         if (parseFiles(storeFilesWithParseErrors)) {
             if (tokenList == null || tokenList.size() < minimumTokenLength) {
                 state = SubmissionState.TOO_SHORT; // parseFiles() didn't fail, so no parse errors found.
@@ -133,10 +133,11 @@ public SubmissionState parse(int minimumTokenLength) {
 
     /**
      * Parse the files of the submission and update state.
+     * @param storeFilesWithParseErrors Whether files with parse errors should be stored.
      * @return Whether parse was successful.
      * @note Successful parse doesn't necessarily imply an {@link SubmissionState#OK OK} state.
      */
-    private boolean parseFiles() {
+    private boolean parseFiles(boolean storeFilesWithParseErrors) {
         if (files == null || files.size() == 0) {
             program.print("ERROR: nothing to parse for submission \"" + name + "\"\n", null);
             return false;
@@ -157,7 +158,7 @@ private boolean parseFiles() {
 
         tokenList = null;
         state = SubmissionState.PARSE_ERRORS; // invalidate submission
-        if (program.getOptions().isDebugParser()) {
+        if (storeFilesWithParseErrors) {
             copySubmission();
         }
         return false;