[Gmod-help] Re: [Gmod-gbrowse] bug report (svg rendering) and feature request

[Lincoln Stein]

Hi Timo,

I had a look at the GD::SVG rendering and realized that the xyplot glyph is
trying to draw lots of fractional-width rectangles. This works in GD (rounds
up to the nearest integer), but not in GD::SVG. Since this is not clearly a
GD::SVG bug, I fixed the glyph so that it works properly with GD:SVG.

To get the fixed code you will have to SVN update to the latest
bioperl-live.

Lincoln

On Wed, Jul 30, 2008 at 7:34 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Timo,
>
> First, I apologize for taking a full month to get back to you.
> Several of us have been on the road for much of July and some things
> fell through the cracks.
>
> I talked with Lincoln and Scott about both the bug and the feature
> request.   First, we think the bug is in GD::SVG, a library used by
> GBrowse.  Please submit a bug report for GD::SVG.  That will help us
> keep track of it.  See
>
>  http://rt.cpan.org/Public/Bug/Report.html?Queue=GD-SVG
>
> for how to do that, or just send an e-mail to bug-GD-SVG at rt.cpan.org.
>
> For the second item, plese file a feature request for GBrowse at
>
>  http://sourceforge.net/tracker/?group_id=27707&atid=391294
>
> Thanks,
>
> Dave C.
> GMOD Help Desk
>
> On Tue, Jul 1, 2008 at 10:45 AM, Timo Sachsenberg
> <timo.sachsenberg at tuebingen.mpg.de> wrote:
> > Hi,
> > I think I stumbled over a bug in the svg rendering module.
> > Check out:
> > http://gbrowse.weigelworld.org/cgi-bin/gbrowse/attax/
> > If I select one raw intensity track and click on High-res image to get
> the svg the wiggle
> > track isn't drawn correctly (nearly all bars are missing).
> >
> > And I'd like to re-request following feature:
> > max_score=16 gets ignored and rounded up to 20. This doesn't make sense
> for log scaled data and explicit definition of max_score in the config file
> should not be ignored.
> >
> > Thanx.
> > Cheers,
> >  Timo
> >
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>
>
>
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-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>

Cold Spring Harbor Laboratory
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Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>
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