Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Colin <col...@gm...>]

Hi Ke,
This is an interesting error. The issue would probably be related to the
new rendering of the "sashimi" style arcs introduced in 1.5.2 (
https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have not
seen this error.

Can you tell me what browser you are using?


I found what I think is a fix here
https://github.com/GMOD/jbrowse-components/pull/2750 but I would still like
to know more info because there are also some possible rendering glitches
in your screenshot (looks like some "intron" lines are drawn on top of
features). If you have data that reproduces this let me know


-Colin



On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> After upgrading to 1.6.4, the CRAM tracks give an error ("e.bezierCurveTo
> is nor function") when rendering coverage plots (the BAM tracks are fine),
> the read alignment rendering part seems to be fine. Here is a screenshot
> and configuration. I'd like to put it here before taking it to github
> issues, maybe there is a simple fix or configuration error on my side.
>
> Thanks!
>
> Ke
>
> [image: ScreenShot.png]
>
>
> {
>       "type": "AlignmentsTrack",
>       "trackId": "SRR11185046_reads",
>       "name": "SRR11185046",
>       "category": [
>         "mRNASeq"
>       ],
>       "assemblyNames": [
>         "Porcine S. scrofa v11.1"
>       ],
>       "adapter": {
>         "type": "CramAdapter",
>         "cramLocation": {
>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>         },
>         "craiLocation": {
>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>         },
>         "sequenceAdapter": {
>           "type": "IndexedFastaAdapter",
>           "fastaLocation": {
>             "uri": "Sscrofa11.1.fa"
>           },
>           "faiLocation": {
>             "uri": "Sscrofa11.1.fa.fai"
>           }
>         }
>       }
>     },
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