Edge case fixes, R implementation of fitness model

[leeprichman]

• multiple edge case fixes
• implementation of greenbaum fitness model in R, return python output and our version
• defer to minimum amplitude value from blast_A or DAI
• add Murine IEDB support, tar already contains new database files.
• try wrappers to temp file removal added

[codecov[bot]]

Codecov Report

Merging #76 into master will increase coverage by 1.61%. The diff coverage is 92.78%.

@@            Coverage Diff             @@
##           master      #76      +/-   ##
==========================================
+ Coverage   94.94%   96.56%   +1.61%     
==========================================
  Files           6        6              
  Lines        2098     2210     +112     
==========================================
+ Hits         1992     2134     +142     
+ Misses        106       76      -30

Impacted Files	Coverage Δ
R/antigen.garnish_jaffa.R	99.49% <ø> (ø)	:arrow_up:
R/antigen.garnish_run.R	83.13% <ø> (ø)	:arrow_up:
R/antigen.garnish_io.R	95.99% <ø> (ø)	:arrow_up:
R/antigen.garnish_assemble.R	99.47% <ø> (ø)	:arrow_up:
R/antigen.garnish_fitness.R	99.19% <100%> (+0.06%)	:arrow_up:
R/antigen.garnish_predict.R	96.16% <91.81%> (+3.75%)	:arrow_up:

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[andrewrech]

@leeprichman I extracted remaining TODO items here to separate package issues. Lets continue editing vignette a bit more then merge if all passes. I added introduction.Rmd back.

[andrewrech]

@davidballi David, would you mind checking that this branch loads on a fresh box before we merge it? Thanks. If you have any suggestions for how to better test that I would love to hear. Currently the tests run on a pre-configured server.

[andrewrech]

@leeprichman great. do you want to pull vignette or edit and try to include in this PR?

[leeprichman]

@andrewrech lets pull vignette and merge. I want these huge updates and fixes out there asap. Vignette will take time to work on that I won't have for a little and I don't want to delay on that. Let me know if you want to merge or I should.

[andrewrech]

merge it if tests pass