Output formats of the CLI

[lafita]

Currently one single output format is provided with the CLI tool, specifying the chain mapping, the number of chains and residues aligned and some scores.

The following outputs, as different files, might be interesting:

1. Global scores file: scores for the global (all-residue alignment).
2. Per chain scores: scores for each chain mapping found.
3. Residue alignment (the equivalent residues between structures).