[DAS] Locations between bases

Thomas Down thomas.a.down at gmail.com
Mon Mar 7 14:41:31 UTC 2011


The day has come when I find I need to be able to distinguish between a
feature which actually *covers* one or a small number of bases (e.g. a SNP)
and a feature which refers to a point between two bases (e.g. an
insertion).  Have any other DAS folk dealt with this before, and if so how?
One possible approach would be something like:

         <START>30000000</START>
         <STOP>29999999</STOP>

...as a way to reference the position between the 29999999th and 30000000th
bases in a sequence... but is this going to break lots of existing client
code?

(I also rather dislike it because there's currently sanity-checking code in
Dazzle to stop you doing stuff like this...)

Any better ideas?

            Thomas.

PS. Yes, I'm aware this is a solved problem in DAS/2.  Afraid I need a DAS/1
solution, though.



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