**DO NOT MERGE** Added features for CompareReferences tool

[orlicohen]

(Linked to #7988)
Feature additions (and integration tests) for CompareReferences tool, including:

• ability to run base-level comparison modes on specified sequences (not just detected mismatching sequences) using "sequences-to-align" option
• changed wording for missing MD5 compatibility status ('COMPATIBLE' to 'MAYBE_COMPATIBLE,' or something similar) in compatibility tool
• option to ignore case level differences in base level comparison modes

NOTE: integration test on using an equivalent sequences input file with more than one line (ie. specifying more than one sequences) not yet tested, and can probably do some refactoring to clean up the code for the equivalent sequence comparisons

[gatk-bot]

Github actions tests reported job failures from actions build 3949939482
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	11.0.11+9	3949939482.12	logs
integration	8	3949939482.0	logs

[codecov]

Codecov Report

Merging #8163 (0eb6ce7) into master (993c7f1) will increase coverage by 0.002%.
The diff coverage is 93.464%.

Additional details and impacted files

@@               Coverage Diff               @@
##              master     #8163       +/-   ##
===============================================
+ Coverage     86.663%   86.665%   +0.002%     
- Complexity     38829     39044      +215     
===============================================
  Files           2331      2337        +6     
  Lines         182003    183104     +1101     
  Branches       19985     20099      +114     
===============================================
+ Hits          157729    158687      +958     
- Misses         17262     17368      +106     
- Partials        7012      7049       +37     

Impacted Files	Coverage Δ
.../hellbender/tools/reference/CompareReferences.java	83.662% <90.741%> (+3.425%)	⬆️
...r/tools/reference/CheckReferenceCompatibility.java	93.204% <100.000%> (+0.067%)	⬆️
...ls/reference/CompareReferencesIntegrationTest.java	81.183% <100.000%> (+5.488%)	⬆️
...hellbender/tools/walkers/annotator/RawGtCount.java	63.415% <0.000%> (-12.195%)	⬇️
...er/utils/MergeAnnotatedRegionsIntegrationTest.java	93.333% <0.000%> (-6.667%)	⬇️
...hellbender/tools/walkers/sv/CollectSVEvidence.java	74.888% <0.000%> (-4.990%)	⬇️
.../scalable/data/LabeledVariantAnnotationsDatum.java	68.421% <0.000%> (-3.801%)	⬇️
...ls/genomicsdb/GenomicsDBImportIntegrationTest.java	84.746% <0.000%> (-3.762%)	⬇️
...vqsr/scalable/LabeledVariantAnnotationsWalker.java	86.822% <0.000%> (-3.696%)	⬇️
.../walkers/haplotypecaller/graphs/InverseAllele.java	59.091% <0.000%> (-3.409%)	⬇️
... and 104 more