Count insertion/deletion events once in pairwise distances

[huddlej]

Description of proposed changes

Counts insertion/deletion (indel) events between sequences as single events instead of counting each gap character independently. Adds logic to support user-defined weights for gaps between specific characters, aggregating weights across all potential mismatches in a sequence-specific distance map, and aggregating weights across all sites in an indel event.

Related issue(s)

Fixes #692

Testing

Adds doctests for the new expected behavior.

[huddlej]

@benjaminotter No worries if you're too busy to check this out, but I thought you might be interested in this Augur module that calculates pairwise distances between sequences. If you find this interesting, you may want to take a shot at issue #693 which adds a similar kind of functionality to augur distance.

[codecov]

Codecov Report

Merging #698 (e392e09) into master (c663c95) will increase coverage by 0.23%.
The diff coverage is 100.00%.

❗ Current head e392e09 differs from pull request most recent head 00fe015. Consider uploading reports for the commit 00fe015 to get more accurate results

@@            Coverage Diff             @@
##           master     #698      +/-   ##
==========================================
+ Coverage   31.28%   31.51%   +0.23%     
==========================================
  Files          41       41              
  Lines        5655     5674      +19     
  Branches     1367     1373       +6     
==========================================
+ Hits         1769     1788      +19     
  Misses       3812     3812              
  Partials       74       74              

Impacted Files	Coverage Δ
augur/distance.py	45.89% <100.00%> (+8.09%)	⬆️

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[huddlej]

@benjaminotter Would you be up for trying to resolve the merge conflicts in this PR? The code this PR modifies overlaps with the code you added to support ignored characters. Tests already exist, so when you get the conflict resolved, you can do the usual ./run_tests.sh to confirm that everything works as expected.

[benjaminotter]

@huddlej, the latest commit resolves the merge conflicts. I used the github interface to do so, which merged master into this branch. I then ran the tests locally and all tests passed.

[huddlej]

Thank you for making these changes and testing them out, @benjaminotter! I'm sorry I forgot to describe the process we use to resolve these types of conflicts. We generally avoid merge commits from master back into a development branch in favor of rebasing the development branch onto master and resolving conflicts during that rebase. This is primarily a Bedford Lab convention (I suspect Richard does not care as much about this, but it's worth checking anyway) that we use to maintain a "clean" git history (so when you look at a graph of the git history, you generally only see development branches like this merged into master with few other merges).

Your edits here were very helpful in confirming the changes that needed to be made, though, and I've used them to perform a rebase onto master and reconfirm that tests passed locally. I'll merge this once it completes the CI.

If you are interested in learning more about how we use git rebase, the git book has a nice chapter on rewriting history and we can also have a quick video chat where I can demo an example of how I use rebase. I didn't get any training in this area of software development during my computer science degree, but it's been super helpful to learn and empowers you to do all kinds of quick git surgery that you'd normally avoid.