Bio/SearchIO/hmmer3: Fix for Bug #3369. Added support to retrieve
the posterior probability line of the alignment using a new
"posterior_string" method. Also removed the skipping of hits
"below_inclusion", to leave it to the user decision. This is working
in hmmscan outputs, but hmmsearch needs more development
Hmmer3: Final fix for Bug #3369. Eliminated the removal of
"inclusion threshold" hits to allow the user to decide.
Also fixed the bug caused by Hmmscan and Hmmsearch reversing
not only the hit and query lines in the alignment, but also
the start-end of Query and Hit. Added more tests.