HMMER: Added support of CS lines in Hmmer2 outputs instead
of ignoring them, which can be retrieved using the method
developed for Hmmer3. This method has changed its name from
"consensus_structure "to "consensus_string" to be consistent
with "query_string", "homology_string", etc.
Hmmer3: For Hmmsearch and Hmmscan, "$hit->length" method will
return the correct length instead of 0 if the "Domain annotation"
line shows a hit coverage of '.]' or '[]'. In this case,
the END position is inferred as the length of the sequence
and the information is added accordingly. Also removed a little
code redundancy. Tests added.
Update to Changes file with the latest fixes