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

[Ke J. <bio...@gm...>]

Hi, Colin,

Thanks for the quick response. I saw this error with both Safari and
Firefox. Now you mention the rendering issue with the intron lines, I did
notice that a while ago. The distinction between BAM and CRAM mentioned in
the original email was not accurate. The error not showing up for the BAM
tracks was because the coverage was continuous in the WGS data, which
happens to be using BAM, while the RNA-Seq data with introns/gaps happens
to be CRAM files.

Thank you very much for fixing this! Since it was a small glitch for
alignment tracks only, I think I'll wait for 1.6.5 to upgrade.

Best.

Ke

On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote:

> 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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