[DAS] Adjacent feature extension

Thomas Down thomas.a.down at gmail.com
Sat Mar 5 15:01:42 UTC 2011


Following on from a discussion at the DAS Workshop:

DAS doesn't have offer any specific support for clients that provide
mechanisms for skipping from the current position to the "next" or
"previous" feature.  I'd like to propose a small extension (one extra filter
option on the existing "features" command) to facilitate this.  Full details
are here:

                 https://github.com/dasmoth/dalliance/wiki/AdjacentFeatures

...but briefly, a request like:

               /das/features?adjacent=chr21:30000000

...would be expected to return a standard DASGFF document containing the two
features either side of the specified point.

All comments are welcome!  One open question is whether the query should *
just* return the adjacent features, or should also return other features
overlapping the adjacent feature.  My preference is for them former, but the
latter does have the merit of being quirk-wards compatible with the existing
feature_id filter.  Does anyone else have strong feelings one way or
another.

There isn't currently a full implementation of this, but if nobody comes up
with major objections, I'm hoping to try implementations in Dazzle (server)
and Dalliance (client) within the next couple of weeks.

                         Thomas.



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