[DAS] Locations between bases

[Ewan Birney]

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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>> http://lists.open-bio.org/mailman/listinfo/das
>
>
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