Replaced CollectFragmentCounts with CollectReadCounts.

[samuelklee]

Closes #4519.

Note that we should still explore and evaluate other collection strategies in the future. However, I think we can go ahead and use this strategy as the default for now.

@asmirnov239 @mbabadi Let's get this merged quick and run the evaluations for the AACR poster using this collection strategy. We should also run some subset of the evaluations with CollectFragmentCounts and check that results improve.

@LeeTL1220 @MartonKN We should rerun the somatic evaluations as necessary to make sure they still look good. We may also want to show any interested parties in CGA the relevant results.

@sooheelee Note that some tutorial material, slides, etc. should be updated at the appropriate time (and may need to be updated again as we continue to tweak the strategy).

[codecov-io]

Codecov Report

Merging #4564 into master will decrease coverage by <.001%.
The diff coverage is 83.333%.

@@               Coverage Diff               @@
##              master     #4564       +/-   ##
===============================================
- Coverage     79.845%   79.845%   -<.001%     
  Complexity     16964     16964               
===============================================
  Files           1062      1062               
  Lines          61691     61676       -15     
  Branches        9984      9983        -1     
===============================================
- Hits           49257     49245       -12     
+ Misses          8544      8539        -5     
- Partials        3890      3892        +2

Impacted Files	Coverage Δ	Complexity Δ
...hellbender/tools/copynumber/DenoiseReadCounts.java	91.892% <ø> (ø)	10 <0> (ø)	⬇️
...ools/copynumber/CreateReadCountPanelOfNormals.java	90% <ø> (ø)	9 <0> (ø)	⬇️
...ools/copynumber/DetermineGermlineContigPloidy.java	96.471% <ø> (ø)	14 <0> (ø)	⬇️
...hellbender/tools/copynumber/GermlineCNVCaller.java	86.364% <ø> (ø)	10 <0> (ø)	⬇️
...hellbender/tools/copynumber/CollectReadCounts.java	85.185% <83.333%> (ø)	10 <5> (?)
...ute/hellbender/utils/read/ArtificialReadUtils.java	92.609% <0%> (-0.87%)	65% <0%> (-2%)
...utils/smithwaterman/SmithWatermanIntelAligner.java	80% <0%> (+30%)	3% <0%> (+2%)	⬆️

[mbabadi]

PR looks good, thanks!