[DAS] Locations between bases

[David Nix]

My two cents...

I'm coming late to this thread so pardon if I missing something but I'd strongly recommend adopting interbase coordinates for DAS/1 (maybe this is already the case?).  This is explicitly specified in DAS/2 spec.  It's pretty critical when it comes to calling SNPs and INDELs.

-cheers, D


On 3/7/11 9:10 AM, "Thomas Down" <thomas.a.down at gmail.com> wrote:

On Mon, Mar 7, 2011 at 4:07 PM, Ewan Birney <birney at ebi.ac.uk> wrote:

>
> 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).
>

Thanks Ewan (+Ed and Andy), that sounds best.  I'm going to need a
non-standard stylesheet glyph to do what I'm after as well, so perhaps it's
best to attach the "interbaseness" to that, rather than the feature itself.


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

Yep, that's not really an option.

            Thomas.
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