[Biococoa-dev] whatsuuup?

Peter Schols peter.schols at bio.kuleuven.be
Wed Oct 5 04:31:59 EDT 2005


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


On 05 Oct 2005, at 01:18, Koen van der Drift wrote:

>
> On Oct 3, 2005, at 11:40 PM, Charles Parnot wrote:
>
>
>>
>> I suppose there would be some positional information, where the  
>> sequence are aligned in some specific ways, so an array of  
>> sequences + an array of offset should do. The best way to start is  
>> to agree on a good, simple but complete and consistent header and  
>> then the implementation almost does not matter and can always be  
>> modified in the future.
>>
>>
>
> I am trying to figure out what you mean by the array of offset. I  
> like to visualize things, so assume we have the following sequences  
> that are related:
>
> 1. CCGTGGGTCCAGGATGA
>
> 2. ----GGGCCAGG----
>
> 3. --GTGGGGCCAGGATGA
>
>
> Then the offset array would be like:
>
> 0, 4, 2
>
>
> But it could also be:
>
> -4, 0, -2
>
>
> Am I on the right track here?
>
>
> - Koen.
>
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