make FASTQ reader remove phred bias from quals

[tedsharpe]

No description provided.

[mwalker174]

Looks straight-forward. Did you want to write a unit test for this?

[tedsharpe]

OK. That would be the right thing to do.

[SHuang-Broad]

:+1
Suggestion: rename the corresponding field in FastqRead as phredQuals?

[codecov-io]

Codecov Report

Merging #4415 into master will increase coverage by 0.033%.
The diff coverage is 54.839%.

@@              Coverage Diff               @@
##              master    #4415       +/-   ##
==============================================
+ Coverage     79.017%   79.05%   +0.033%     
- Complexity     16447    16449        +2     
==============================================
  Files           1047     1047               
  Lines          59186    59189        +3     
  Branches        9672     9672               
==============================================
+ Hits           46767    46789       +22     
+ Misses          8664     8639       -25     
- Partials        3755     3761        +6

Impacted Files	Coverage Δ	Complexity Δ
.../hellbender/tools/spark/sv/utils/SVFastqUtils.java	72.139% <54.839%> (+7.493%)	7 <2> (+2)	⬆️
...bender/tools/walkers/mutect/FilterMutectCalls.java	95.833% <0%> (ø)	7% <0%> (ø)	⬇️
...itute/hellbender/tools/walkers/mutect/Mutect2.java	92% <0%> (ø)	15% <0%> (ø)	⬇️
...park/sv/discovery/alignment/AlignmentInterval.java	89.655% <0%> (+0.383%)	73% <0%> (ø)	⬇️
...nder/utils/runtime/StreamingProcessController.java	70.37% <0%> (+0.823%)	50% <0%> (ø)	⬇️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	80% <0%> (+1.29%)	39% <0%> (ø)	⬇️

[tedsharpe]

added round-trip test that fails without the fix.
responded to rename request with explicit documentation instead.