Aligning to multiple genomes/chromosomes

• Input to index is a file of file names (fofn) that allows to provide the indexer w/ multiple reference files
• Updated internals to account for the multiple reference sequences
• Mapper outputs alignment positions as ref_id:position where ref_id is a [0;n-1] integer referring to the reference sequences (total of n) in the order they were given in fofn.

added bin dir to makefile

0.0.2

added development docker

Test release to integrate w/ docker

0.0.1

added docker files for dev image; timing aligner w/o IO