[BioC] homopolymer gap extension penalty in Biostrings

[Noah Hoffman]

Hello Herve,

Thanks a lot for your suggestions - we are indeed doing exactly what you suggested (as Fred noted) with respect to run length encoding - and it's nice to see that this is so conveniently done using IRanges.

> Also, I'm still not clear about this:
>> 
>> Another thing that would be useful would be per-strand gap creation
>> and gap extension penalties.

What I meant here (and didn't express very clearly) is the idea that we may believe that one sequence in a pairwise alignment (sequence 1, for example a pyrosequencing read) is more likely to contain insertions than the other (sequence 2, eg a known primer sequence). In this case it would be useful to specify a different penalties for gap opening or extension in each sequence. 

Thanks a lot,
Noah