Bugfix to GTF/GFF and jbrowse

Author: bbimber

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

@@ -790,12 +790,12 @@ private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, Referen
 
     public boolean needsProcessing()
     {
-        return (needsGzip() && !isGzipped()) || doIndex() || shouldHaveFreeTextSearch();
+        return (needsGzip() && !isGzipped()) || shouldBeReSorted() || doIndex() || shouldHaveFreeTextSearch();
     }
 
     public boolean shouldBeCopiedToProcessDir()
     {
-        return (needsGzip() && !isGzipped());
+        return (needsGzip() && !isGzipped()) || shouldBeReSorted();
     }
 
     public boolean isGzipped()
@@ -837,7 +837,7 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
         }
 
         File targetFile = expData.getFile();
-        if (needsGzip() && !isGzipped())
+        if ((needsGzip() && !isGzipped()) || shouldBeReSorted())
         {
             //need to gzip and tabix index:
             if (processedTrackFile.exists() && !SequencePipelineService.get().hasMinLineCount(processedTrackFile, 1))
@@ -1165,6 +1165,17 @@ else if (TRACK_TYPES.gff.getFileType().isType(finalLocation) || TRACK_TYPES.gtf.
         }
     }
 
+    private boolean shouldBeReSorted()
+    {
+        String sourceFilename = getSourceFileName();
+        if (sourceFilename == null)
+        {
+            return false;
+        }
+
+        return TRACK_TYPES.gff.getFileType().isType(sourceFilename) || TRACK_TYPES.gtf.getFileType().isType(sourceFilename) || TRACK_TYPES.bed.getFileType().isType(sourceFilename);
+    }
+
     public File getLocationOfProcessedTrack(boolean createDir)
     {
         ExpData expData = getExpData();