[DAS] Locations between bases

[Andy Jenkinson]

Oh Thomas, why do you do it to us?

May I ask what the specific application is? Depending on what you need, an insertion can be modelled with a feature covering both bases with a specific glyph (or type).

I think what you propose is a common approach, but it is very likely going to break things for some clients (or at least give undefined results). Some additional element would be more compatible.

On 7 Mar 2011, at 14:41, Thomas Down wrote:

> 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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