BQSR: restore ability to specify custom covariates and to disable standard covariates

[droazen]

Added a quick-and-dirty temporary port of RepeatLengthCovariate
to test this functionality.

Resolves #4568

[droazen]

Not ready for merge yet! Needs tests + some additional fixes for AnalyzeCovariates. The basic BaseRecalibrator -> ApplyBQSR pipeline with a custom covariate seems to be working, however.

@takutosato please try this branch out with your new homopolymer covariate and let me know whether it works! Feel free to grab some time on my calendar next week for help working through any issues.

[codecov-io]

Codecov Report

Merging #4688 into master will increase coverage by 0.015%.
The diff coverage is 55.33%.

@@               Coverage Diff               @@
##              master     #4688       +/-   ##
===============================================
+ Coverage     79.842%   79.857%   +0.015%     
- Complexity     17332     17497      +165     
===============================================
  Files           1074      1075        +1     
  Lines          62924     63442      +518     
  Branches       10182     10341      +159     
===============================================
+ Hits           50240     50663      +423     
- Misses          8704      8783       +79     
- Partials        3980      3996       +16

Impacted Files	Coverage Δ	Complexity Δ
...ecalibration/covariates/QualityScoreCovariate.java	88.889% <ø> (ø)	12 <0> (+1)	⬆️
...s/recalibration/covariates/ReadGroupCovariate.java	96.429% <ø> (ø)	12 <0> (+1)	⬆️
...ils/recalibration/covariates/ContextCovariate.java	92.727% <ø> (ø)	35 <0> (+1)	⬆️
...nder/utils/recalibration/covariates/Covariate.java	100% <ø> (ø)	1 <0> (ø)	⬇️
...utils/recalibration/covariates/CycleCovariate.java	97.674% <ø> (ø)	22 <0> (+1)	⬆️
...forms/bqsr/BaseRecalibratorEngineSparkWrapper.java	0% <0%> (ø)	0 <0> (ø)	⬇️
...nder/tools/spark/BaseRecalibratorSparkSharded.java	22.807% <0%> (ø)	2 <0> (ø)	⬇️
...ellbender/tools/walkers/bqsr/BaseRecalibrator.java	82.609% <0%> (-5.763%)	11 <1> (ø)
...ender/utils/recalibration/RecalibrationReport.java	88.718% <100%> (+0.778%)	61 <0> (-1)	⬇️
...r/utils/recalibration/BaseRecalibrationEngine.java	87.143% <100%> (ø)	67 <0> (ø)	⬇️
... and 16 more

[droazen]

@takutosato Have you had a chance to try this branch out with your new covariate yet?

[takutosato]

@droazen sorry I've been working on my other project but am hoping to spend some time on this on Friday!

[droazen]

@takutosato Just checking in -- had a chance to try this branch out yet with your covariate?

[takutosato]

@droazen had to set this aside a little but I'm going to work on it today!

[droazen]

@takutosato What's the status of this? Do you still need this feature?