Diagonal based alignment improvements

Diagonal filtering improvements

Correctness and overall speed have been improved:

• A special case of longest path was ignored
• A better definition of optimal path has made possible some additional filtering, thus reducing the search space and time complexity
• A better implementation of path storage, using a traceback vector has reduced the memory footprint'
• A garbage collection like method has been added to reduce the number of iterations dedicated to paths collections maintenance

Other fixes

• A common case for stale kmers in the minimizing window was not taken into account
• In the regular Multiple Sequence Alignment procedure, a bug was preventing the detection of gap openings. The formulae for computing gap opening/closing penalty has been fixed.