[DAS] DAS spec clarifications

[Steve Chervitz]

Some issues came up in our internal discussion at Affymetrix about DAS that I'd
like clarification on:

* Should the server perform a logical AND or an OR when a feature command
specifies both type and category?

* It would be nice if the feature command permitted method specification in
addition to type and category. This would enhance the usefulness of the method
information you get back from the types command.

* Does a server have to deal in 1-based sequence coordinates to be
DAS1-compliant? I'm assuming yes, but it would be good to state so explicitly
in the spec. This is relevant to a recent thread on the Bioperl list: 

http://bioperl.org/pipermail/bioperl-l/2002-July/008318.html

Internally, we make much use of 0-based half-open intervals (or "inter-base"
coordinates as we call them, where the numbers refer to the positions
in-between the bases). It would be great if a server could specify the
coordinate system it uses. It would then be up to the client to do the
appropriate conversion if necessary. Perhaps something for DAS2?

Steve

=====
Steve Chervitz
sac@bioperl.org

__________________________________________________
Do You Yahoo!?
Yahoo! Health - Feel better, live better
http://health.yahoo.com