[DAS] Locations between bases

[Suzanna Lewis]

+1

On Mar 7, 2011, at 8:38 AM, David Nix wrote:

> 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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