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Searchable annotation tracks are not working #1227

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hrehrauer opened this issue Nov 19, 2020 · 10 comments
Closed

Searchable annotation tracks are not working #1227

hrehrauer opened this issue Nov 19, 2020 · 10 comments

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@hrehrauer
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We load our own reference together with bed and gtf files. Things worked fine but now we get the error this.config.browser is undefined and the features are in the end displayed but not searchable. fyi. our code is:

`

            <title>igv.js</title>
            
            <!-- IGV JS-->
           
            <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"></script>
              
              </head>
              
              <body>
              
              
              <div id="igv-div" style="padding-top: 10px;padding-bottom: 10px; border:1px solid lightgray"></div>
                
                <script type="text/javascript">
                  
                  document.addEventListener("DOMContentLoaded", function () {
                    
                    const config =
                      {
                        reference: {
                          id: "GRCm38.p6",
                          fastaURL: "https://fgcz-gstore.uzh.ch/reference/Mus_musculus/GENCODE/GRCm38.p6/Sequence/WholeGenomeFasta/genome.fa",
                          indexURL: "https://fgcz-gstore.uzh.ch/reference/Mus_musculus/GENCODE/GRCm38.p6/Sequence/WholeGenomeFasta/genome.fa.fai",
                          wholeGenomeView: true
                        },
                        tracks: [
                          {
                            type: 'alignment',
                            format: 'bam',
                            url: 'https://fgcz-gstore.uzh.ch/projects/p3397/STAR_51639_2020-11-13--20-37-31/PTcre-_PM3.bam',
                            indexURL: 'https://fgcz-gstore.uzh.ch/projects/p3397/STAR_51639_2020-11-13--20-37-31/PTcre-_PM3.bam.bai',
                            samplingDepth: '2000',
                            alignmentRowHeight: 10,
                            colorBy: "strand",
                            name: 'PTcre-_PM3',
                            showSoftClips: true,
                            filter: {duplicates: false}
                          },
                          {
                            name: "Genes",
                            type: "annotation",
                            format: "gtf",
                            sourceType: "file",
                            url: "https://fgcz-gstore.uzh.ch/reference/Mus_musculus/GENCODE/GRCm38.p6/Annotation/Release_M23-2019-11-05/Genes/transcripts.only.gtf",
                            displayMode: "EXPANDED",
                            name: "GRCm38.p6 Genes",
                            searchable: true
                          },
                          {                                     
                            name: "exons",    
                            type: "annotation",
                            format: "bed",    
                            sourceType: "file",
                            url: "https://fgcz-gstore.uzh.ch/reference/Mus_musculus/GENCODE/GRCm38.p6/Annotation/Release_M23-2019-11-05/Genes/genes.bed",
                            displayMode: "EXPANDED",
                            name: "GRCm38.p6 Exons",
                            searchable: true  
                          }
                        ]
                      };
                    
                   const igvDiv = document.getElementById("igv-div"); 
                    igv.createBrowser(igvDiv, config)
                    .then(function (browser) {
                      console.log("Created IGV browser");
                    })
                    
                  });
                
                </script>
                  
                  </body>
                  
                  </html>

`

Can you please help? The error message is:
TypeError: this.config.browser is undefined value textFeatureSource.js:233 e textFeatureSource.js:224 h runtime.js:63 _invoke runtime.js:293 S runtime.js:118 gr runtime.js:747 o runtime.js:747
Best
Hubert
@jrobinso
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Which version of igv.js are you using?

@hrehrauer
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We are using
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"></script>
best
hubert

@hrehrauer
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In fact we are unsure, if we should run our own igv.js or if it is save to refer to your server?
best
hubert

@jrobinso
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Running from the server is fine, that is a permanent URL for that release. Version 2.7.1 is a very recent release, I'm searching now to see when this bug was introduced.

@jrobinso
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I found the problem and it will be fixed in this weekends release (2.7.2). In the meantime, do you recall the release you were using that was working? It looks like 2.6.8 should not have this problem, but I'm not certain.

jrobinso added a commit that referenced this issue Nov 19, 2020
@jrobinso
Bug fix -- annotation tracks not searchable. See issue #1227
e6a0555
@jrobinso jrobinso changed the title error: this.config.browser is undefined Searchable annotation tracks are not working Nov 19, 2020
@hrehrauer
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unfortunately, I don't know the release that was still working. ;-(
We probably used it succesfully in September.
many thanks
hubert

@jrobinso
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Well the fix ill be released this weekend, as 2.7.2, but if you need a faster solution the "2.6.8" version should work.

@hrehrauer
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thanks. we will give it a try next week.
best
hubert

jrobinso added a commit that referenced this issue Nov 22, 2020
@jrobinso
"Bug fix -- annotation tracks not searchable. See issue #1227"
c1ace18 
This reverts commit e6a0555, try a different approach.
@hrehrauer
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any news on when it will be rolled out?

@jrobinso
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Just released as 2.7.2

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@jrobinso @hrehrauer