dalliance

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There's quite a bit of code scattered around to handle canonicalization of chromosome names for the "22" vs. "chr22" case. We should - try to centralize this in one place...

dasmoth

Is it possible to add Wormbase genome version 235? Available here: ftp://ftp.wormbase.org/pub/wormbase/releases/WS235/species/c_elegans/

danielecook

New stylesheet system

1

The current BioDAS-heritage stylesheet system is reaching its limits. - Neither the DAS XML syntax nor the Biodalliance-specific "JSON" syntax (which is really just a serialisation of how we represent...

dasmoth

When you add multiple Blob VCF sources, the same blob is displayed twice

1

Here's what my `sources` array looks like: ``` javascript var sources = [ { name: 'Genome', twoBitURI: 'http://www.biodalliance.org/datasets/hg19.2bit', tier_type: 'sequence' }, { name: 'VCF1', tier_type: 'memstore', payload: 'vcf', // uri:...

danvk

Now seen two independent cases of servers sniffing the headers of BAM files and adding "Content-Encoding: gzip" or similar, causing the browser to uncompress them.

dasmoth

Add "trackIdle" and "allTracksIdle" callbacks

2

It would be nice to get some kind of notification when a track has finished loading, regardless of whether it's the initial load or triggered by a call to `browser.setLocation`.

danvk

Tooltips aren't centered

1

e.g. on the biodalliance.org page, when I hover over the "

danvk

When you display a BAM track, dalliance has to load a large (often 10+ MB) BAM index file before it can display anything. It would be nice to give some...

danvk

Add mate pair and strand information to pileup view

1

hammer

Human GRCh37/hg19 turns into all T's

2

To reproduce: - Visit http://www.biodalliance.org/human37.html - Type in "20:2,684,623..2,684,723" and hit enter to zoom to that part of chr20 - Click & drag to scroll to the left. Eventually you...

danvk