[DAS] DAS spec clarifications

[Lincoln Stein]

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

This should be treated as an OR.  I will fix the specification to
reflect that.

 > * 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.

Quite right.

 > * 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?

You are right that 1-based closed intervals are used.  Possibly this
is something that could be made optional in DAS2, but I would prefer
to pick a single coordinate system convention and stick to it.
I agree that Interbase coordinates are better than the current
convention in Bioperl and elsewhere.

Lincoln

 > 
 > Steve
 > 
 > =====
 > Steve Chervitz
 > sac@bioperl.org
 > 
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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