TypeError: indexedFastaStore is null

[billzt]

I don't know why. Three month later it is OK. And I haven't use it for a long time. Today when I try to open it, nothing happened. After I check the console log, it says:

GCContent plugin starting                          main.js:15:9
FeatureSequence plugin initialized.            main.js:41:9
FeatureSequence will try to rock this with no_store              main.js:149:9
store 'no_store' not found                                           dojo.js:78:205
TypeError: indexedFastaStore is null                        main.js:155:15

Here is my config file (part):

      {
         "urlTemplateFAI" : "seq/genome_Ghir_JBrowse.fa.fai",
         "key" : "Reference sequence",
         "useAsRefSeqStore" : true,
         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
         "urlTemplate" : "seq/genome_Ghir_JBrowse.fa",
         "category" : "Reference sequence",
         "type" : "SequenceTrack",
         "label" : "DNA"
      },

      {
         "style" : {
            "className" : "feature"
         },
         "menuTemplate" : [
            {},
            {},
            {},
            {
               "iconClass" : "dijitIconBookmark",
               "content" : "function(track,feature){return track.browser.plugins.FeatureSequence.callFxn(track, feature); }",
               "action" : "contentDialog",
               "label" : "View Feature Sequence"
            }
         ],
         "key" : "Principle Transcript",
         "onClick" : {
            "url" : "../search/transcript_details.php?transcript_id={id}",
            "action" : "newWindow",
            "label" : "View Details of Transcript <b>{id}</b>"
         },
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/principle_transcript/{refseq}/trackData.jsonz",
         "compress" : 1,
         "category" : "Feature Annotation",
         "type" : "CanvasFeatures",
         "label" : "principle_transcript"
      },

What's wrong? I don't think I've changed any configuration these three months.

[billzt]

Well, the problem seems that we must show reference sequence tracks first, and then it would be OK.

[twsaari]

Yes, this is due to that patch that I did for you a few months ago (It allowed you to use the indexed fasta). It loads the refseq store from your browser's cache. That's why you need to load the reference sequence first, so that your browser has it loaded into cache. Then the plugin can determine which track is the reference sequence - and finally get sequence from the refseq store.

I'm not sure, but I think newer versions of JBrowse have addressed the issue with the indexed fasta store not being named correctly. In this case, we could just undo the aforementioned patch, because it would not be needed anymore. I'll check on that and see.

[billzt]

Thanks. I think nowdays we would add this to manual.