Change raw MQ to a tuple of (sumSquaredMQs, totalDepth) for better ac…

[ldgauthier]

…curacy where there are lots of uninformative reads

[ldgauthier]

@jamesemery the only way I could get genomicsDB tests to pass was to upgrade to the latest version and use the protobuf implementation for the vidmap by merging in #4993. That PR is blocked because I asked for allele-specific features and it's looking like no one is going to do that anytime soon. But if you'd rather merge that first and then rebase this to keep things tidy, I understand.

[codecov-io]

Codecov Report

Merging #5237 into master will decrease coverage by 0.006%.
The diff coverage is 85.308%.

@@               Coverage Diff               @@
##              master     #5237       +/-   ##
===============================================
- Coverage     86.798%   86.791%   -0.006%     
- Complexity     29711     29731       +20     
===============================================
  Files           1820      1820               
  Lines         137406    137517      +111     
  Branches       15160     15174       +14     
===============================================
+ Hits          119265    119353       +88     
- Misses         12637     12656       +19     
- Partials        5504      5508        +4

Impacted Files	Coverage Δ	Complexity Δ
...ute/hellbender/utils/variant/GATKVCFConstants.java	80% <ø> (ø)	4 <0> (ø)	⬇️
...e/hellbender/utils/variant/GATKVCFHeaderLines.java	99.338% <100%> (+0.004%)	10 <0> (ø)	⬇️
...ute/hellbender/tools/FixCallSetSampleOrdering.java	72.807% <100%> (+0.735%)	25 <0> (+1)	⬆️
...er/tools/walkers/GenotypeGVCFsIntegrationTest.java	78.261% <100%> (+2.651%)	25 <6> (+6)	⬆️
.../hellbender/tools/genomicsdb/GenomicsDBImport.java	78.088% <63.158%> (-1.011%)	52 <1> (ø)
...der/tools/walkers/annotator/RMSMappingQuality.java	83.607% <78.182%> (-10.208%)	41 <27> (+1)
...der/tools/genomicsdb/GenomicsDBImportUnitTest.java	86.207% <80%> (-6.101%)	9 <0> (ø)
...ls/genomicsdb/GenomicsDBImportIntegrationTest.java	89.176% <85.714%> (-0.206%)	75 <3> (+2)
...der/tools/walkers/CombineGVCFsIntegrationTest.java	87.931% <87.5%> (+0.158%)	24 <2> (+1)	⬆️
...institute/hellbender/engine/FeatureDataSource.java	79.032% <89.655%> (+1.962%)	52 <6> (+6)	⬆️
... and 5 more

[jamesemery]

@ldgauthier To clarify, the code here is just ported over from #4969 correct? Could we make the protobuff changes a separate branch and merge #4969 in afterwards?

[ldgauthier]

This went in as #4969 after upgrading GenomicsDB, making this PR a dupe.