[Bioperl-l] SiteMatrix changes

[skirov]

>===== Original Message From Sendu Bala <bix at sendu.me.uk> =====
>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.
It is OK, I also realize that my documentation sucks and might be quite 
confusing with respect to some of the options (not to mention some wrong 
assumptions I have made)... 
Stefan
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