feat: output umi grouping metrics

[znorgaard]

Closes #1020

This PR optionally emits a new metric file with read filtering statistics generated by GroupReadsByUmi.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.65%. Comparing base (1c96bd7) to head (6b427fe).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1021   +/-   ##
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  Coverage   95.64%   95.65%           
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  Files         126      126           
  Lines        7395     7403    +8     
  Branches      498      521   +23     
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+ Hits         7073     7081    +8     
  Misses        322      322           

Flag	Coverage Δ
unittests	95.65% <100.00%> (+<0.01%)	⬆️

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[clintval]

A few final suggestions from me. Looks good!

@tfenne or @nh13 do you want to give a pass?

[clintval]

Suggested change

	// TODO: Create a more comprehensive test case
	// TODO: Consider creating more unit tests that vary the following metric fields

[nh13]

@znorgaard how about adding to existing tests? E.g.

fgbio/src/test/scala/com/fulcrumgenomics/umi/GroupReadsByUmiTest.scala

Line 426 in e1dcbab

it should "exclude reads that contain an N in the UMI" in {

[znorgaard]

@nh13, just add the metric generation and check to those other tests?

That would work. I generally like to see a "complex" test case where non-zero values are generated for each metric entry all at once. But, in this specific case we're pulling from existing variables, so individual tests might be good enough.