filter: Fix duplicates from force inclusions

[victorlin]

Description of proposed changes

This fixes double-writing of the same record in output files.

Related issue(s)

• Fixes filter: --include/--include-where leads to duplicate entries in outputs #985

Testing

Tests added. See checks before and after fix.

[codecov]

Codecov Report

Merging #986 (d97611f) into master (f07cc5f) will decrease coverage by 0.02%.
The diff coverage is 100.00%.

❗ Current head d97611f differs from pull request most recent head 5def1a7. Consider uploading reports for the commit 5def1a7 to get more accurate results

@@            Coverage Diff             @@
##           master     #986      +/-   ##
==========================================
- Coverage   59.22%   59.20%   -0.03%     
==========================================
  Files          50       50              
  Lines        6259     6260       +1     
  Branches     1586     1586              
==========================================
- Hits         3707     3706       -1     
- Misses       2290     2292       +2     
  Partials      262      262              

Impacted Files	Coverage Δ
augur/filter.py	95.74% <100.00%> (-0.37%)	⬇️

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[joverlee521]

I haven't completely grasped what happens in augur filter but the test outputs and overall change makes sense to me. I only left a non-blocking question and comment.