[DAS] Locations between bases

[Ewan Birney]

I'd say this is start=end, and a convention that this indicates the  
point
to the left or the right with a glyph. With this converntion for the  
edge case one either
has to allow the 0 base (right based insertion convention, insertion  
at the very
start) or end+1 position (left based insertion convention, insertion  
at the
every end).


I know, this triggers doing things on inter-base coordinates, but  
that's just
a big, big change.



On 7 Mar 2011, at 16:03, Thomas Down wrote:

> Well, that's a separate debate, and I don't really want to open it  
> at the moment.
>
> However, right now I am thinking quite specifically of visualization  
> issues.  Once you're zoomed in to base-pair resolution, there is a  
> meaningful distinction between "on a base" and "between a base".
>
> Andy: what I'm trying to model is insertion sites.  I guess that's  
> the main use for this kind of thing.
>
>                Thomas.
>
>
>
> On Mon, Mar 7, 2011 at 3:26 PM, Ewan Birney <birney at ebi.ac.uk> wrote:
>
> I also note that this is stretching DAS's mindset away from
>
>   "DAS is to support visualisation of data on clients for human  
> users to read"
>
> to
>
>   "DAS semantically represents things accurately for programmatic  
> decisions"
>
>
> I think one is better off keeping these things separate.
>
>
>
> On 7 Mar 2011, at 15:21, Andy Jenkinson wrote:
>
> 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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