Remove unneeded usages of GATKRead defensive getters

[magicDGS]

To improve performance, mostly in the trimming pipeline but also in the quality checks for reads, this commit change the usages of the default GATKRead getters in favor of the unsafe getters versions (when modifications are not expected).

Closes #461

[codecov[bot]]

Codecov Report

Merging #476 into master will decrease coverage by 0.005%. The diff coverage is 100%.

@@               Coverage Diff               @@
##              master      #476       +/-   ##
===============================================
- Coverage     93.417%   93.412%   -0.005%     
  Complexity       991       991               
===============================================
  Files             95        95               
  Lines           2643      2641        -2     
  Branches         284       284               
===============================================
- Hits            2469      2467        -2     
  Misses           133       133               
  Partials          41        41

Impacted Files	Coverage Δ	Complexity Δ
...former/trimming/ApplyTrimResultReadTransfomer.java	100% <100%> (ø)	10 <2> (ø)	:arrow_down:
.../read/transformer/trimming/MottQualityTrimmer.java	100% <100%> (ø)	6 <1> (ø)	:arrow_down:
...ls/read/transformer/trimming/TrailingNtrimmer.java	100% <100%> (ø)	2 <1> (ø)	:arrow_down:
.../read/transformer/CheckQualityReadTransformer.java	100% <100%> (ø)	6 <0> (ø)	:arrow_down:

[codecov[bot]]

Codecov Report

Merging #476 into master will decrease coverage by 0.005%. The diff coverage is 100%.

@@               Coverage Diff               @@
##              master      #476       +/-   ##
===============================================
- Coverage     93.417%   93.412%   -0.005%     
  Complexity       991       991               
===============================================
  Files             95        95               
  Lines           2643      2641        -2     
  Branches         284       284               
===============================================
- Hits            2469      2467        -2     
  Misses           133       133               
  Partials          41        41

Impacted Files	Coverage Δ	Complexity Δ
...agicdgs/readtools/utils/trimming/TrimmingUtil.java	97.436% <ø> (ø)	14 <0> (ø)	:arrow_down:
...former/trimming/ApplyTrimResultReadTransfomer.java	100% <100%> (ø)	10 <2> (ø)	:arrow_down:
.../read/transformer/CheckQualityReadTransformer.java	100% <100%> (ø)	6 <0> (ø)	:arrow_down:
...ls/read/transformer/trimming/TrailingNtrimmer.java	100% <100%> (ø)	2 <1> (ø)	:arrow_down:
.../read/transformer/trimming/MottQualityTrimmer.java	100% <100%> (ø)	6 <1> (ø)	:arrow_down: