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 <[email protected]> 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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