Engine read caching.

[cmnbroad]

Allow tools to opt-in for read caching (enabled in this PR for CNNScoreVariants and FilterAlignmentArtifacts) when issuing forward-only queries such as those used to query a ReadsContext for all reads backing each variant.

The cache matches the (sometimes surprising - see https://github.com/broadinstitute/gatk/issues/4901) results that are returned when caching is not used, specifically that an unmapped but placed read that is mated with a mapped read is only returned if the start position overlaps the interval query interval, whereas the mapped read is returned if any part of the read overlaps the query interval.

[codecov-io]

Codecov Report

Merging #4902 (bedd108) into master (c6eb337) will increase coverage by 68.201%. The diff coverage is 91.690%.

:exclamation: Current head bedd108 differs from pull request most recent head 3db7949. Consider uploading reports for the commit 3db7949 to get more accurate results

@@               Coverage Diff                @@
##              master     #4902        +/-   ##
================================================
+ Coverage     18.644%   86.845%   +68.201%     
- Complexity      4635     32366     +27731     
================================================
  Files           1261      1994       +733     
  Lines          73745    149492     +75747     
  Branches       11768     16506      +4738     
================================================
+ Hits           13749    129826    +116077     
+ Misses         57944     13642     -44302     
- Partials        2052      6024      +3972     

Impacted Files	Coverage Δ
...e/hellbender/engine/FeatureDataSourceUnitTest.java	88.318% <ø> (ø)
...institute/hellbender/engine/FeatureDataSource.java	74.603% <57.143%> (+24.603%)	:arrow_up:
...ender/engine/cache/SideReadInputCacheStrategy.java	81.481% <81.481%> (ø)
...adinstitute/hellbender/engine/ReadsDataSource.java	91.667% <84.615%> (+33.333%)	:arrow_up:
...ellbender/engine/VariantWalkerIntegrationTest.java	87.288% <86.667%> (ø)
...engine/cache/DrivingFeatureInputCacheStrategy.java	88.000% <88.000%> (ø)
...ellbender/engine/cache/LocatableCacheUnitTest.java	96.471% <96.471%> (ø)
...gumentcollections/ReadInputArgumentCollection.java	87.500% <100.000%> (+20.833%)	:arrow_up:
...org/broadinstitute/hellbender/engine/GATKTool.java	87.719% <100.000%> (+19.135%)	:arrow_up:
...titute/hellbender/engine/cache/LocatableCache.java	100.000% <100.000%> (ø)
... and 1863 more

[cmnbroad]

Rebased this to do some testing with current master.