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

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

Fix released in 1.6.5 :)

Thanks again for reporting!


-Colin

On Wed, Feb 16, 2022 at 3:45 PM Colin <col...@gm...> wrote:

> Excellent, thank you for reporting the issue! We should have a new version
> out soon
>
>
> -Colin
>
> On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote:
>
>> 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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>>>>
>>>