Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[Mitch S. <mit...@be...>]

CHAN, KENNETH 1 [AG/7721] wrote:
> Hi guys,
>   I encountered a strange result when using wig-to-json.pl. The
> quantitative track I got has a very low resolution and the values
> doesn't seem like corresponding to the wiggle file.

Hi, I haven't gotten a chance to reproduce this or look at it in detail 
yet, but I do have a quick answer to part of this:

Currently, JBrowse renders wiggle files up to one pixel per base 
(because that's the highest possible data density) and then uses the web 
browser to stretch the images when the user is zoomed in closer than one 
pixel per base.  On large genomes, this saves a lot of disk space and 
processing time compared to rendering images at higher resolutions.  
Plus, JBrowse allows for variable font sizes, so at the highest zoom 
level, different users will have different values for the number of 
pixels per base.  So even if we wanted to generate higher resolution 
images, we wouldn't be able to pick a scale factor for the highest zoom 
level that would work exactly for everyone; in many cases the web 
browser would still have to stretch or shrink the image.

Originally, the web browsers all used a scaling algorithm that kept the 
results crisp-looking, but more recently they've started to use a 
smoother (bicubic) scaling algorithm by default, and wiggle tracks 
started looking fuzzy in JBrowse when they're zoomed in all the way.

The web browsers have just started implementing switches that will allow 
us to specify the old scaling method:
https://developer.mozilla.org/en/CSS/image-rendering

and writing the JBrowse code to set that value appropriately is on our 
to-do list (although if anyone wants to tackle it, that would be 
welcome; it should be simple to set the relevant CSS styles on the 
images in ImageTrack.js).

Mitch