Generate lucene index stats with JBrowse

Author: bbimber

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -993,12 +993,25 @@ private void prepareLuceneIndex(Logger log) throws PipelineJobException
             return;
         }
 
+        File indexDir = getExpectedLocationOfLuceneIndex(false);
+        if (indexDir != null && indexDir.exists())
+        {
+            try
+            {
+                FileUtils.deleteDirectory(getExpectedLocationOfLuceneIndex(false));
+            }
+            catch (IOException e)
+            {
+                throw new PipelineJobException(e);
+            }
+        }
+
         List<String> args = runner.getBaseArgs("VcfToLuceneIndexer");
         args.add("-V");
         args.add(getExpData().getFile().getPath());
 
         args.add("-O");
-        args.add(getExpectedLocationOfLuceneIndex(false).getPath());
+        args.add(indexDir.getPath());
 
         List<String> infoFieldsForFullTextSearch = getInfoFieldsToIndex();
         for (String field : infoFieldsForFullTextSearch)
@@ -1009,6 +1022,9 @@ private void prepareLuceneIndex(Logger log) throws PipelineJobException
 
         args.add("--allow-missing-fields");
 
+        args.add("--index-stats");
+        args.add(getExpectedLocationOfLuceneIndexStats(false).getPath());
+
         JSONObject config = getExtraTrackConfig();
         if (config != null && !config.isNull("lenientLuceneProcessing") && config.getBoolean("lenientLuceneProcessing"))
         {
@@ -1351,6 +1367,11 @@ public boolean shouldHaveFreeTextSearch()
         return json != null && json.optBoolean("createFullTextIndex", false);
     }
 
+    public File getExpectedLocationOfLuceneIndexStats(boolean throwIfNotFound)
+    {
+        return new File(getExpectedLocationOfLuceneIndexStats(throwIfNotFound).getPath() + ".stats.txt");
+    }
+
     public File getExpectedLocationOfLuceneIndex(boolean throwIfNotFound)
     {
         File basedir = getLocationOfProcessedTrack(false);