On Jul 17, 2009, at 9:43 AM, Christopher Lee wrote:
> > On Jul 16, 2009, at 9:50 PM, C. Titus Brown wrote: > >> -> > -> 2. handling of self-alignment in pairwise mode. We proposed >> -> > changing >> -> > -> pairwise mode to report self-alignments, rendering obsolete >> the >> -> > -> current annoying warning message. >> >> Am I correct that this boils down to setting bidirectionalRule=None >> in >> the NLMSA constructor? > > No. We just need to add a conditional that retains self-alignments > under our desired condition, in the NLMSASlice.__init__(). I'll > have to look at the code to see exactly where. I think it'll be > easier for me to just make the change and push it to the simpleframe > branch for your approval... Hi Titus, I implemented our proposed change to allow NLMSAs in pairwiseMode to report self-matches (which previously were filtered out), and removed the annoying warning message from BlastMapping. I also updated the blast tests to check for this new behavior; under the new versions of the tests, the old behavior (filtering out self-matches) would be reported as an *error*. The actual code change for the new behavior was simple (change one line of a conditional), and all tests pass, so I pushed it to master. -- Chris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
