[Bioperl-l] SearchIO::waba

[Jason Stajich]

(Main trunk) Added a waba parser to Bio::SearchIO.  Still an early version
so don't rely on it yet, but help test.  Test in t/WABA.t rather than
pushing SearchIO tests over 700.  Might be asking a bit much to stuff waba
alignments into Results->Hits->HSPs but I think it works.  A couple of
assumptions are made and I might want to rearrange the Query to Hit/HSP
relationship so that all Hits for a Query (even if they come later in the
result file) are aggregated into the same HSP under the same Hit name.

-jason
-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu