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

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

Thanks for pointing this out, there was a regression where the fix for this
got undone. Will post a fix soon!

-Colin

On Wed, Jun 1, 2022 at 12:48 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> After upgrading to 1.7.8, this problem seems to be back. In both Firefox
> and Safari, the coverage part of the CRAM rendering would give a reload
> error: "TypeError: e.bezierCurveTo is not a function". Maybe the "sushimi"
> code is not compatible with some recent updates?
>
> Thanks!
>
> Ke
>
> On Fri, Feb 18, 2022 at 3:13 PM Colin <col...@gm...> wrote:
>
>> 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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>>>>>>
>>>>>