Implement a sequence alignment tool (with no threading yet)

[bjclavijo]

Implement an alignment tool that uses a non-unique skip-mer/k-mer index and a delta filtering as in the long read mapper.
Once implemented, the long read mapper can used for the non-filtered alignments if that level of integration can be attained. Not before.
Input of sequences as a fasta file for an API a plus.
Annotation of the sequences in classes (taking to features) another plus.

Once this is done a rework of the threader can be the next logical step.

[bjclavijo]

This requires to have moved the indexes into the SDG, then just implement an aligner object that takes an DG. (so that eventually we can do threading alignment too).