Smith-Waterman algorithm implementation under Apache 2

[lopozz]

PR for #125

Improvements from the previous version of the alignment.py:

• improved readability of the code
• removed global variables (match_award, mismatch_penalty, gap_penalty)
• introduced reference to algorithm
• apache 2.0 licence

In writing this implementation I decided to respect the signature of the original script to have a drop-in replacement for the algorithm. No additional dependencias were introduced.

The demo.py script was run successfully

Optionally I also wrote unit tests on the old script to compare it with my implementation. I could also commit those to maintain consistency in case of future PRs