Unpaired

Here, I've added an unpaired option and several tests for its use. I have not changed how the "good," "bad," or "pc_good" etc. metrics have been calculated, so currently these measures do not reflect this addition. I have made a few name rearrangements for the alignment stats to reflect the addition. The nomenclature is most apparent when you view the report in order.

    bundle exec bin/transrate -a test/data/sorghum_transcript.fa -l test/data/150uncovered.l.fq -i test/data/150uncovered.r.fq -u test/data/150uncovered.u.fq

I hope you like the addition :) Let me know what I can do to make it more robust.