juliema/TRAM — pull request #64 by daisieh (2013-11-20 02:30:47+00:00)
Title: Cleaning hit matrix logic and cumulative hits

I realized that I could simplify the logic a great deal if I returned the hash directly from findsequences and just used the names of the contigs to query the hash. I then realized that I could clean it up even more and get rid of the unused hit_matrices array by using the hit_matrix hash as a cumulative hash of every good result and save arrays of the relevant contig_names as needed.