io: Migrate VCF functions from filter+utils to io

[victorlin]

Description of proposed changes

See commit messages.

Motivated by work in #854.

Related issue(s)

N/A

Testing

Tests moved accordingly.

[codecov]

Codecov Report

Merging #929 (4279b66) into master (9dda176) will increase coverage by 0.02%.
The diff coverage is 50.53%.

@@            Coverage Diff             @@
##           master     #929      +/-   ##
==========================================
+ Coverage   59.59%   59.61%   +0.02%     
==========================================
  Files          43       43              
  Lines        6056     6059       +3     
  Branches     1550     1550              
==========================================
+ Hits         3609     3612       +3     
  Misses       2188     2188              
  Partials      259      259              

Impacted Files	Coverage Δ
augur/io_support/shell_command_runner.py	91.66% <ø> (ø)
augur/utils.py	65.10% <ø> (+8.20%)	⬆️
augur/io.py	62.60% <43.90%> (-37.40%)	⬇️
augur/align.py	89.04% <100.00%> (+0.05%)	⬆️
augur/filter.py	96.19% <100.00%> (-0.13%)	⬇️
augur/index.py	87.50% <100.00%> (-0.18%)	⬇️
augur/mask.py	100.00% <100.00%> (ø)
augur/translate.py	38.18% <100.00%> (+0.24%)	⬆️
augur/tree.py	51.10% <100.00%> (ø)

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[huddlej]

Good call. These functions always felt odd to have in filter.py. Since we are moving these functions, I'd slightly prefer to move then into io.py, to keep them close to other I/O logic.

[victorlin]

@huddlej done: 4279b66. io.py is getting a little hairy – I have other changes I'd like to make but will put those in another PR.