Multiple Reference Contigs in one Alignment Visualization

[josiahseaman]

As a user, I want to get a visualization that shows the alignment between all of chr22 including chr22 unplaced contigs.

Currently, the ChainParser runs a one-to-many relationship. This could be upgraded to many-to-many by continuing to append to self.ref_seq_gapped after one "chromosome" has already been sequenced. This will probably look like using self.read_contigs() on the reference sequence as well and using the FASTA file as the definition of the list of contigs (chromosomes) to be processed. This would be an alternative to listing out specific contig names on the command line.

This issue will be addressed after #33 is done to cut back on the immense proliferation of contig headers in the visualization.