* DO NOT MERGE * adding base level comparison modes for CompareReferences tool

[orlicohen]

[gatk-bot]

Github actions tests reported job failures from actions build 2841114156 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	11	2841114156.13	logs
integration	11	2841114156.12	logs
unit	8	2841114156.1	logs
integration	8	2841114156.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2841313433 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	11	2841313433.13	logs
integration	11	2841313433.12	logs
unit	8	2841313433.1	logs
integration	8	2841313433.0	logs

[codecov[bot]]

Codecov Report

Merging #7987 (b8e168e) into master (c22972a) will decrease coverage by 31.524%. The diff coverage is 3.205%.

:exclamation: Current head b8e168e differs from pull request most recent head b4ffbc2. Consider uploading reports for the commit b4ffbc2 to get more accurate results

Additional details and impacted files

@@               Coverage Diff                @@
##              master     #7987        +/-   ##
================================================
- Coverage     52.260%   20.735%   -31.524%     
+ Complexity     29146     12332     -16814     
================================================
  Files           2310      2331        +21     
  Lines         180344    181988      +1644     
  Branches       19840     19985       +145     
================================================
- Hits           94247     37736     -56511     
- Misses         80124    140700     +60576     
+ Partials        5973      3552      -2421     

Impacted Files	Coverage Δ
...bender/tools/reference/ReferenceSequenceTable.java	79.570% <ø> (-7.527%)	:arrow_down:
...ute/hellbender/utils/alignment/MummerExecutor.java	0.000% <0.000%> (ø)
...ls/reference/CompareReferencesIntegrationTest.java	0.694% <0.000%> (-76.770%)	:arrow_down:
.../hellbender/tools/reference/CompareReferences.java	21.344% <3.429%> (-45.323%)	:arrow_down:
...bender/utils/alignment/MummerExecutorUnitTest.java	8.696% <8.696%> (ø)
...der/tools/reference/CompareReferencesUnitTest.java	12.500% <12.500%> (ø)
...tute/hellbender/tools/reference/ReferencePair.java	79.487% <50.000%> (-10.256%)	:arrow_down:
...rg/broadinstitute/hellbender/tools/CountBases.java	0.000% <0.000%> (-100.000%)	:arrow_down:
...rg/broadinstitute/hellbender/tools/CountReads.java	0.000% <0.000%> (-100.000%)	:arrow_down:
...g/broadinstitute/hellbender/utils/mcmc/Decile.java	0.000% <0.000%> (-100.000%)	:arrow_down:
... and 1329 more

[gatk-bot]

Github actions tests reported job failures from actions build 2842345810 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	11	2842345810.12	logs
integration	8	2842345810.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2842334324 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	11	2842334324.12	logs
integration	8	2842334324.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2849712241 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	11	2849712241.13	logs
integration	11	2849712241.12	logs
unit	8	2849712241.1	logs
integration	8	2849712241.0	logs

[orlicohen]

CompareReferences FullAlignment integration tests & ExecuteMummer unit test failing currently due to MUMmer build