[Biococoa-dev] whatsuuup?

[Charles Parnot]

> I'm not sure if I get it right, but the offset could become quite  
> complex because for sequences with many indels there will be many  
> offsets and you not only need to store offset length but also  
> offset position. For example:
>
> 1. CCGTGGGTCCAGGATGA
>
> 2. ----GGG---CCA--GG----
>
> The offset array for 2. could be something like (0,4); (8,3);  
> (14,2); (17,4)
> Maybe we could have an NSOffset (or NSInsertion) struct similar to  
> NSPoint that has two integers: position and length.
>
> Charles, is this what you meant with offset information?
>
> Peter

You are going too fast for me, guys! NSRange is one possibility, as  
suggested by Koen.
The other possibility is to remember that BCSymbol includes a gap  
symbol, that can be used for that, too, without the need for all the  
intermediate offsets.

It does not matter too much in the end, though it might make our life  
easier to use the gap symbol to get the information back to the user  
of the framework, for instance when we need to return a string with  
the sequence, including the gaps.

charles

--
Xgrid-at-Stanford
Help science move fast forward:
http://cmgm.stanford.edu/~cparnot/xgrid-stanford

Charles Parnot
charles.parnot at gmail.com