Some existing IGV pages fail with "Uncaught (in promise) TypeError: t.chromosomeOrder.split is not a function"

whoisthatdog commented 8 months ago

At some point the default genomes file at https://s3.amazonaws.com/igv.org.genomes/genomes.json was updated such that chromosomeOrder became a list rather than a string. This causes older versions of IGVjs (in my case, 2.5.2) to fail with the above error.

One of the great things about IGVjs is that I can send biologists self-contained HTML files with their data mapped to the genome. Unfortunately this error means that no existing file will work without updating the HTML - something that they will not know how to do. Can this change be rolled back?

jrobinso commented 8 months ago

This should be fixed now, give it a try.

jrobinso commented 8 months ago

@whoisthatdog BTW your application of igv.js sounds interesting, would you be willing to share more? Are you using igv-reports? You can respond, if you wish, to igv-team@broadinstitute.org. Thanks.

whoisthatdog commented 8 months ago

Thanks for the quick response. The files do work now, but it pops up this error dialog. Once cleared the browser seems fully functional.

I'll follow up on the application over email, thanks.

jrobinso commented 8 months ago

That's curious, anything in the console log? Can you can provide me with a test html that reproduces this?

whoisthatdog commented 8 months ago

The console reports this:

Here is a test file that reproduces it on my system. It does not appear with IGV version 2.15.11. Thanks much.

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <title>Human Oligo Design Map 2024-02-05</title>
    <script src='https://cdn.jsdelivr.net/npm/igv@2.5.2/dist/igv.min.js'></script>
</head>
<body>
<div id="igv", style="height: 500;">

</div>

<script>
    let igvDiv = document.getElementById('igv')

    const genome = 'hg38';

    let options = {
        genome: 'hg38',
        name: "Human (GRCh38/hg38)",
        fastaURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
        indexURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
        cytobandURL: "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",
        showKaryo: true,
        locus: 'GAPDH',
        trackDefaults: {
            annotation: {
                autoHeight: true
            }
        },
        tracks: [
            {
                name: "Gencode v28",
                type:'annotation',
                nameField:'transcript_id',
                format: "gtf",
                url: "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/gencode.v28.basic.annotation.sorted.gtf.gz",
                indexURL: "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/gencode.v28.basic.annotation.sorted.gtf.gz.tbi",
                visibilityWindow: -1,
                removable: true,
                order: 99999
            },
            {
                name: "Controls",
                order: 10,
                features: [
                    {'chr':'chr12','start':6537775,'end':6537795,'name':'GAPDH ASO','score':0,'strand':'-','exons':[{'start':6537775,'end':6537795}]}
                ],
                displayMode: "EXPANDED",
                format: "gtf"
            }
        ]
    }

    igv.createBrowser(igvDiv, options)
        .then(function (browser) {

        })

</script>
</body>
</html>

jrobinso commented 8 months ago

Ahh, yes that error is a particular problem with the refseq annotations for hg38. It should be fixed soon, its a data file problem. See https://github.com/igvteam/igv/issues/1482

igvteam / igv.js

Some existing IGV pages fail with "Uncaught (in promise) TypeError: t.chromosomeOrder.split is not a function" #1761