[DAS2] Refinements to range attribute and query filters in spec

Helt,Gregg Gregg_Helt at affymetrix.com
Thu Feb 9 23:18:42 UTC 2006

In the latest spec, the format for range queries is 
and the format for range attributes in feature elements is 
In the earlier spec
(http://biodas.org/documents/das2/das2_get.html#ranges) everything but
the seqid component of the range query was optional.  Are min and max
still optional, as in these examples from the previous version of the
    Chr1/1000     Chr1 beginning at position 1000 and going to the end.
    Chr1/:2000    Chr1 from the start to position 2000.
I personally find these kind of ranges confusing and not particularly
useful, and would rather make min and max required for both the range
attribute and range-based query filters. 
Also, the latest spec states: 
A region may be on the forward or reverse strand or on both strands.
These are respectively denoted 1, -1 and 0.  The reverse strand is the
reverse complement of the forward strand.  Unspecified strand means
forward strand.
So for a features query, are the four overlap filters below equivalent?
Or does the addition of strand information further filter the returned
features by strand?  But if that's the case, then according to the spec
having no strand specified means forward.  So that would mean
overlaps="Chr1/1000:2000" would only return forward strand annotations,
and not any on the reverse strand?  To me that's counterintuitive, from
a filtering perspective I'd rather no strand info mean "both strands".
My main point though is we need to be explicit about how strand info or
lack thereof affects features queries with range-based filters.

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