First pull request: --genome feature, --unpaired feature [incomplete]

Please let me know if you have suggestions for revisions and additional tests. I am very happy to work on this. Thank you for your time.

I have added some minor adjustments to existing classes/methods, one new class, and its tests.

1. The first change is the addition of the new class and option --genome, which permits the alignment of the assembled transcripts to the genome with crb-blast. This is useful for identifying misassembly in the transcriptome or genome, reporting the number of unaligned and aligned transcripts and the average percent homology. The feature is optional to the execution of the program. 
2. The second change is the addition of a new option to the executable: --unpaired, which permits the alignment of unpaired fastq reads to the assembly. These reads can be aligned with or instead of paired end reads. This option can also be ommitted to align only paired reads. This function is incomplete owing to the statistical calculations for which it was made. I suggest a revised read_metrics that assesses alignment rate of all reads, paired reads, and combined summary statistics based on all reads.


Changes:
* lib files
    1. bin/transrate
    2. bowtie2
    3. comparative_metrics
    4. read_metrics
    5. reference_alignment
    6. transrater
    7. transrate.rb
* test files
    1. test_bin
    2. test_bowtie
    3. test_reference_alignment
    4. test_transrater
* data files
    1. test_ref_align_assembly
    2. test_ref_align_genome