Mutation profiling and shmulate vignette

[Jason Vander Heiden]

We could use a vignette covering basic mutation analysis and the shmulate functions. Not necessarily for v0.1.3. It can wait until v0.1.4, if needed.

[Jason Vander Heiden]

The mutation component is done.

[Jason Vander Heiden]

Merging #99:

http://shazam.readthedocs.io/en/version-0.1.8---mutation-profiling-enhancements/vignettes/Mutation-Vignette/#calculate-mutations-within-subregions-of-the-v-segment

Might be clearer to add a bit of text to separate the usage of IMGT_V vs IMGT_V_BY_REGIONS in calculating FWR/CDR mutation frequencies.

[Jason Vander Heiden]

Issue #99 was marked as a duplicate of this issue.

[Julian Zhou]

Additional note on IMGT_V vs. IMGT_V_BY_REGIONS etc. in mutation profiling vignette: commit 8b642a7.

Shmulate vignette: commit c620fc5