[DAS] plans for 1.6 release
thomas.a.down at gmail.com
Thu Sep 2 16:35:21 UTC 2010
On Tue, Aug 31, 2010 at 5:28 PM, Andy Jenkinson <andy.jenkinson at ebi.ac.uk>wrote:
> Hi all,
> As many of you know, DAS version 1.6 has been in development for a while
> now, and we would really like to get it out of the door and "official". To
> this end, we aim to do the following:
> 1. resolve the remaining questions over the current draft (principally,
> alignments and categorize) *
> 2. ensure core Java and Perl software libraries support the specification
> 3. officially switch over ***
> 4. developers of solid client and server implementations will announce
> dates for 1.6 support
I agree that it'll be nice to get this out, although I'm still kind-of
nervous about setting changes in stone when there aren't already
implementations out there (client-side, in particular). Are there any
client developers who've had a good poke around and can reassure me?
The other concern (which I've only just noticed, and had some discussions
off-list with Andy) is that -- in the new PART/PARENT system -- it is
explicitly stated that you'll only get features overlapping the query
region. Features outside the query region will be excluded even if they're
PARTs of something that is included (e.g., you'll only get a subset of exons
for a gene).
To my mind, the biggest advantage of a feature hierarchy system over the
GROUP system it replaces is that you can guarantee that you'll get the
complete dataset for a complex feature in a single fetch. I note that the
DAS/2 spec (which has a very similar PART/PARENT system) takes the opposite
approach and states that you'll always get complete graphs of features back.
Given that this is a new (to DAS/1) system, is there any reason not to do
things the DAS/2 way?
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