[ensembl-dev] BED file format on custom track

[Anne Lyle]

Hi Liam

As I suspected, there was a logic error in the validation code. I’m just pushing the fix out to our servers this afternoon.

Regards

Anne



Anne Lyle
Senior Ensembl Web Developer
EMBL-EBI, Wellcome Trust Genome Campus
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494178



> On 6 Oct 2016, at 14:29, Liam Thompson <dejmail at gmail.com> wrote:
> 
> Hi Anne
> 
> I retried the GFF file on the Genoverse browser, and it loads fine and displays correctly (albeit in need of some tweaking), but still no luck on Ensembl.
> 
> I have uploaded the file in case you want to see what is different with it, compared to the validator does.
> 
> http://textuploader.com/dabl6
> 
> Kind regards
> Liam
> 
> On 2016-10-06 11:36, Anne Lyle wrote:
>> Hi Liam
>> 
>> BED should be fine - I’ll have a look at your file and see if there’s some reason it’s breaking our validator. The validation is quite new code, so there may be an error in its logic.
>> 
>> Cheers
>> 
>> Anne
>> 
>> 
>>> On 5 Oct 2016, at 19:01, Liam Thompson <dejmail at gmail.com> wrote:
>>> 
>>> Hi Anne
>>> 
>>> Thanks for the reply. I'm working from a Linux system, but not sure that
>>> makes any difference.
>>> 
>>> I have just tried it on Firefox v. 49, and the uploader just doesn't
>>> seem to go anywhere, so I can confirm that behaviour. It also happens in
>>> Private mode, so it's not a plugin.
>>> 
>>> I tried in Google Chrome (53.0.2785.143 (64-bit)) normal and
>>> Private/Incognito mode and the same thing happens.
>>> 
>>> Is there another file format you would recommend that I can use to
>>> display short sequences of interest in a track in the genome browser ?
>>> 
>>> Kind regards
>>> Liam
>>> 
>>> 
>>>> ------------------------------
>>>> 
>>>> Message: 2
>>>> Date: Wed, 5 Oct 2016 17:14:57 +0100
>>>> From: Anne Lyle <annelyle at ebi.ac.uk>
>>>> Subject: Re: [ensembl-dev] BED file format on custom track
>>>> To: Ensembl developers list <dev at ensembl.org>
>>>> Message-ID: <3FBA2DBE-8EB3-4317-9785-A1FD61902772 at ebi.ac.uk>
>>>> Content-Type: text/plain; charset=utf-8
>>>> 
>>>> Hi Liam
>>>> 
>>>> Are you using Firefox (version 49) by any chance? We?ve seen some upload issues in this browser, so it could be related. If not, I?ll have a look at your file and see if there?s any reason why our parser isn?t reading it correctly.
>>>> 
>>>> Cheers
>>>> 
>>>> Anne
>>> 
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>> 
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