Hi Kanwei,
Could you check and commit the following three changesets from my new branch:
http://bitbucket.org/peterjc/galaxy-central/src/blastplus_nov24
i.e. these three changesets:
http://bitbucket.org/peterjc/galaxy-central/changeset/8f0e5a169630 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469
This address a problem found earlier today by Alex Bossers (CC'd) while testing the BLAST+ wrappers. The problem can occur when when the query sequence is masked (with XXXX characters), this broke my calculation of the identity and mismatch counts (failing an assert statement I'd included as a sanity check). The new unit test is a cut down version of his failing example.
Note that in order to run the unit tests, you will need to first re-enable the tool in tools_conf.xml.sample - the converter tests does not depend on the BLAST+ binaries being installed.
Thank you,
Peter