bioperl/bioperl-live — pull request #48 by pcantalupo (2012-10-31 13:13:55+00:00)
Title: Fixed Bug 3343 by correctly calculating the total gaps

Hello,

I've updated Bio/SearchIO/blasttable.pm to fix bug 3343 and t/SearchIO/blasttable.t to test it. The only side effect that I see is that when running the blasttable.t tests, a warning now appears: MSG: Did not define the number of conserved matches in the HSP; assuming conserved == identical (247) . I believe the warning is normal because of the fact that the number of conserved matches in an HSP for blasttable output is not known.

Thank you,

Paul