gmod-ajax

Re: [Gmod-ajax] JBrowse: Strange peaks appear in WIG tracks

[Ian H. <ih...@be...>]

Hi David,

We did receive your email - thanks.

There is actually a lighthouse ticket for this issue already, though it 
is somewhat cryptic:

http://jbrowse.lighthouseapp.com/projects/23792/tickets/19-handle-wiggle-regions-that-span-tile-boundaries

If you get a chance, it'd be great if you could post your files for 
recreating the issue as a comment/footnote to this ticket (I would do 
this myself but I seem to have misplaced your original email unfortunately)

Best wishes
Ian



On 10/11/10 4:41 AM, David Breimann wrote:
> Hello again,
>
> I just wanted to verify you have received this email.
>
> Best,
> Dave
>
> On Wed, Oct 6, 2010 at 10:59 PM, David Breimann<dav...@gm...>wrote:
>
>> Hi Mitch,
>>
>> I didn't send this to the mailing list to avoid sharing the large files
>> with everyone, but feel free to cc your reply to the list.
>>
>> I've encountered a strange phenomena: some peaks appear in tracks created
>> from WIG files with no apparent reason. The WIG doesn't have any value that
>> supports a "peak" in those positions.
>>
>> Recreate the situation:
>> * start with a clean JBrowse clone.
>> * prepare-refseq with the attached fasta file (in the archive).
>> * wig-to-json with the attached WIG file (in the archive).
>> * Now zoom in to position 68000. Attached is a print-screen of what I see.
>> Inspect the WIG and see all the values at this area are 2-3 and there's no
>> peak.
>>
>> Keep up the good work!
>> Dave
>>
>

Re: [Gmod-ajax] Fwd: JBrowse: Strange peaks appear in WIG tracks

[Ian H. <ih...@be...>]

Thanks David. I just committed a fix and closed the ticket. Best wishes, Ian

David Breimann wrote:
> 
> The files are attached again. I hope you'd be able to recreate and solve 
> the issue.
> 
> Thanks,
> Dave
> 
> 
> ---------- Forwarded message ----------
> From: *David Breimann* <dav...@gm... 
> <mailto:dav...@gm...>>
> Date: Wed, Oct 6, 2010 at 10:59 PM
> Subject: JBrowse: Strange peaks appear in WIG tracks
> To: Mitch Skinner <mit...@be... 
> <mailto:mit...@be...>>
> Cc: Ian Holmes <ih...@be... <mailto:ih...@be...>>
> 
> 
> Hi Mitch,
> 
> I didn't send this to the mailing list to avoid sharing the large files 
> with everyone, but feel free to cc your reply to the list.
> 
> I've encountered a strange phenomena: some peaks appear in tracks 
> created from WIG files with no apparent reason. The WIG doesn't have any 
> value that supports a "peak" in those positions.
> 
> Recreate the situation:
> * start with a clean JBrowse clone.
> * prepare-refseq with the attached fasta file (in the archive).
> * wig-to-json with the attached WIG file (in the archive).
> * Now zoom in to position 68000. Attached is a print-screen of what I 
> see. Inspect the WIG and see all the values at this area are 2-3 and 
> there's no peak.
> 
> Keep up the good work!
> Dave
> 
> 
> 
> ------------------------------------------------------------------------
> 

Re: [Gmod-ajax] Fwd: JBrowse: Strange peaks appear in WIG tracks

[David B. <dav...@gm...>]

Thank you very much Ian.

On Tue, Oct 12, 2010 at 1:38 AM, Ian Holmes <ih...@be...> wrote:

> Thanks David. I just committed a fix and closed the ticket. Best wishes,
> Ian
>
> David Breimann wrote:
>
>>
>> The files are attached again. I hope you'd be able to recreate and solve
>> the issue.
>>
>> Thanks,
>> Dave
>>
>>
>> ---------- Forwarded message ----------
>> From: *David Breimann* <dav...@gm... <mailto:
>> dav...@gm...>>
>> Date: Wed, Oct 6, 2010 at 10:59 PM
>> Subject: JBrowse: Strange peaks appear in WIG tracks
>> To: Mitch Skinner <mit...@be... <mailto:
>> mit...@be...>>
>> Cc: Ian Holmes <ih...@be... <mailto:ih...@be...>>
>>
>>
>> Hi Mitch,
>>
>> I didn't send this to the mailing list to avoid sharing the large files
>> with everyone, but feel free to cc your reply to the list.
>>
>> I've encountered a strange phenomena: some peaks appear in tracks created
>> from WIG files with no apparent reason. The WIG doesn't have any value that
>> supports a "peak" in those positions.
>>
>> Recreate the situation:
>> * start with a clean JBrowse clone.
>> * prepare-refseq with the attached fasta file (in the archive).
>> * wig-to-json with the attached WIG file (in the archive).
>> * Now zoom in to position 68000. Attached is a print-screen of what I see.
>> Inspect the WIG and see all the values at this area are 2-3 and there's no
>> peak.
>>
>> Keep up the good work!
>> Dave
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>>

Re: [Gmod-ajax] JBrowse: Strange peaks appear in WIG tracks

[Ian H. <ih...@be...>]

PS, I believe all we will really need is the WIG file
If you can re-send this I will try to fix it today
Best, Ian

On 10/11/10 10:44 AM, Ian Holmes wrote:
> Hi David,
>
> We did receive your email - thanks.
>
> There is actually a lighthouse ticket for this issue already, though it
> is somewhat cryptic:
>
> http://jbrowse.lighthouseapp.com/projects/23792/tickets/19-handle-wiggle-regions-that-span-tile-boundaries
>
> If you get a chance, it'd be great if you could post your files for
> recreating the issue as a comment/footnote to this ticket (I would do
> this myself but I seem to have misplaced your original email unfortunately)
>
> Best wishes
> Ian
>
>
>
> On 10/11/10 4:41 AM, David Breimann wrote:
>> Hello again,
>>
>> I just wanted to verify you have received this email.
>>
>> Best,
>> Dave
>>
>> On Wed, Oct 6, 2010 at 10:59 PM, David Breimann<dav...@gm...>wrote:
>>
>>> Hi Mitch,
>>>
>>> I didn't send this to the mailing list to avoid sharing the large files
>>> with everyone, but feel free to cc your reply to the list.
>>>
>>> I've encountered a strange phenomena: some peaks appear in tracks created
>>> from WIG files with no apparent reason. The WIG doesn't have any value that
>>> supports a "peak" in those positions.
>>>
>>> Recreate the situation:
>>> * start with a clean JBrowse clone.
>>> * prepare-refseq with the attached fasta file (in the archive).
>>> * wig-to-json with the attached WIG file (in the archive).
>>> * Now zoom in to position 68000. Attached is a print-screen of what I see.
>>> Inspect the WIG and see all the values at this area are 2-3 and there's no
>>> peak.
>>>
>>> Keep up the good work!
>>> Dave
>>>
>>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax