bioperl/bioperl-live — pull request #45 by yinjun111 (2012-10-02 19:34:12+00:00)
Title: Simplealign

Hi, Chris,

This is the up-to-date Bio::SimpleAlign module. I have integrated all the changes from the live bioperl repo.

Bio::SimpleAlign and t/Align/SimpleAlign2.t should be the only modules changed compared to the live bioperl repo. You can just drag these two scripts to your branch.

t/Align/SimpleAlign2.t is a new testing script for Bio::SimpleAlign. You can compare the results to the old testing script t/Align/SimpleAlign.t. The new testing script includes new tests for the new methods in Bio::SimpleAlign. Because there are some potential bugs in the old method, you will see 12 tests failed in the old test t/Align/SimpleAlign.t by using the new Bio::SimpleAlign package. I will explain why in the email.

Cheers,
Jun