SNV caller analysis part 1 revamp

[cansavvy]

Purpose/implementation

This PR implements a few smaller changes that were initially discussed and implemented on a retired PR #159.

Changes in this PR:

1. Makes the regional analysis optional throughout the pipeline.
   • Adds as an optparse option in both 01-calculate_tmb_vaf.R and in 02-run_eval.R
   • Employs the --no_region option in run_caller_evals.sh
2. Fixes a chromosome labeling problem with the COSMIC file.
   • Chromosome's X and Y were labeled as 23 and 24 though our data has them as X and Y.

Issue

For SNV caller comparison #161, #103 and Tumor Mutation Burden #3 and sort of #11

Directions for reviewers

Are these changes implemented well?
Does everything seem to be in order?

Is there a better way for me to have the non-regional report as opposed to having a whole other copy of that template? I do not like having the whole thing repeated but am unsure as to an alternative?

Results

No new results from these changes.

Docker and continuous integration

*These changes do not require new packages or new CircleCI tests. *

• Run a linter
• Set the seed- I didn't, but let me know if I should.
• Comments and/or documentation up to date
• Double check your paths
• Spell check any Rmd file or md file
• Restart R and run all notebooks fresh and save

[jashapiro]

As as making your template flexible, you could break it into pieces. One file with the main section, one file with the region analysis section, then a session info section file. You would then cat them together on the fly. But I don't necessarily think that is worth the effort, especially for this stage of analysis.

[jashapiro]

Looks good. Just a couple little things.

[jashapiro]

Approved!