[Bioperl-l] SiteMatrix changes

[Sendu Bala]

aaron.j.mackey at gsk.com wrote:
> Lastly, it is rather poor form to swoop down on some piece of code and 
> fundamentally alter the way it behaves without warning and discussion. 
> Presumably you had to change the test suite to get the new behavior to 
> pass tests, which is always a sign that some form of discussion needs to 
> happen (e.g. perhaps backwards compatibility is an issue).

Yes, I should have discussed it with Stefan first. Stefan: I apologize. 
In my defense, it simply looked like a bug that needed fixing, and the 
tests that needing changing were only those that expected the wrong 
answers that the code was mistakenly generating.