Fix epydoc markup (see _Probcons.py for working example)
Use epydoc markup for Clustal Omega wrapper (for pretty doctest)
SearchIO: Correctly parse empty consensus lines in hmmer2 parser

Hmmer2TextParser.read_next() usually reads over lines only containing
whitespace. The original code to deal with the consensus line would already
turn off the strip() call, so the consensus lines would come out in the
correct length. However, if the consensus line was completely empty,
read_next() would erroneously skip over the consensus line.
This fix disables the empty line skip when whitespace stripping is
turned off.

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
SearchIO: Add padding to consensus line if needed.

hmmer2 seems to leave out the spaces of an empty consensus line.
Add padding for the consensus line if needed.

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Merge remote-tracking branch 'upstream/master' into samtools_wrapper