GenericHSP: Added '.' to gap symbols in "_pre_gaps",
since is now used by HMMER3 format in alignments

GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
to return undef if the query/hit length is unknown (like in
some HMMER outputs), to avoid division by 0 crashes.
Added this new behaviour to documentation and will include some
tests for hmmer in next commit.
Hmmer3: Fixed wrong capture of homology line from alignment
when it had flanking whitespaces. Added the calculation
of HSP alignment length, and number of identical and conserved
residues directly from the homology line. Also added several
tests to check for these new features.
infernal.t: Addition of '.' to gap symbols showed that some tests
where ignoring gaps in query lines. Fixed the tests.
GenericHSP: Refined "_pre_gaps" to not use '.' for ERPIN,
who have both symbols in the line but only '-' represents
the gap.