Added flags to create genomebam file with kallisto bus

[ricomnl]

kallisto bus has the following optional options:

--genomebam               Project pseudoalignments to genome sorted BAM file
-g, --gtf                     GTF file for transcriptome information
                              (required for --genomebam)
-c, --chromosomes             Tab separated file with chromosome names and lengths
                              (optional for --genomebam, but recommended)

This PR adds parameters to kb count so that one can use the --genomebam flag as well as a gtf file and optionally a chromosomes file to output a .bam file. A test is added to make sure the functionality works as intended.

[ricomnl]

@sbooeshaghi @Lioscro this would be a useful addition IMO because BAM files are required for downstream tasks like genetic demultiplexing. Right now, one would have to use cellranger to get bam files. In addition, the PR would solve this previous issue #147

[Yenaled]

@ricomnl I am the person currently making major upgrades to and maintaining kallisto. Thanks for the pull request. I have several updates I need to make first but I will try to merge this pull request when I can. Don't worry -- it's on my radar.

[Lioscro]

As long as the commands printed from --dry-run looks reasonable, the changes lgtm.

[Yenaled]

@Lioscro all looks good to me; feel free to merge