count SNPs in modify

[nevrome]

Closes #298 when merged.

[codecov]

Codecov Report

❌ Patch coverage is 56.52174% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 52.55%. Comparing base (c4e87bc) to head (68b58a5).

Files with missing lines	Patch %	Lines
src/Poseidon/CLI/Trident/Modify.hs	61.90%	8 Missing and 8 partials ⚠️
...Poseidon/CLI/Trident/OptparseApplicativeParsers.hs	0.00%	4 Missing ⚠️

Additional details and impacted files

@@                  Coverage Diff                   @@
##           rectifyModifySplit     #408      +/-   ##
======================================================
+ Coverage               52.53%   52.55%   +0.01%     
======================================================
  Files                      38       38              
  Lines                    6129     6165      +36     
  Branches                  654      661       +7     
======================================================
+ Hits                     3220     3240      +20     
- Misses                   2255     2264       +9     
- Partials                  654      661       +7     

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[stschiff]

Excellent, thanks for implementing this, very useful! You haven't added a golden test, which is fine... have you tested it yourself?

[nevrome]

I tried it in the community-archive, yes, and also added a basic golden test now.

Could you quickly confirm that my use of getJointGenotypeData is approrpiate, and that there is no chance that the order of counts would not match the order of samples in the .janno file? My implementation is so simple that I'm worrying about missing something here.