Validation of sequence dictionaries from multiple BAMs now throws warning instead of exception in CNV workflows.

[samuelklee]

Unfortunately, projects like TCGA with BAMs from different sequencing centers do not use the exact same sequence dictionary across them. I've relaxed validation in cases where dictionaries are checked across different BAMs so that only a warning is thrown; however, cases where dictionaries should arise from the same BAM still throw an exception.

[codecov-io]

Codecov Report

Merging #4758 into master will decrease coverage by 0.012%.
The diff coverage is 23.077%.

@@              Coverage Diff               @@
##              master    #4758       +/-   ##
==============================================
- Coverage     80.052%   80.04%   -0.012%     
  Complexity     17413    17413               
==============================================
  Files           1080     1080               
  Lines          63099    63100        +1     
  Branches       10196    10201        +5     
==============================================
- Hits           50512    50505        -7     
- Misses          8597     8599        +2     
- Partials        3990     3996        +6

Impacted Files	Coverage Δ	Complexity Δ
...r/arguments/CopyNumberArgumentValidationUtils.java	59.42% <0%> (-7.744%)	17 <0> (-2)
...ute/hellbender/tools/copynumber/ModelSegments.java	98.404% <33.333%> (-1.061%)	44 <0> (ø)
...ools/copynumber/DetermineGermlineContigPloidy.java	94.048% <33.333%> (-2.423%)	14 <0> (ø)
...hellbender/tools/copynumber/GermlineCNVCaller.java	84.404% <33.333%> (-1.96%)	10 <0> (ø)
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+40%)	3% <0%> (+2%)	⬆️

[samuelklee]

See #3864. Closing that issue. @LeeTL1220 can you take a look at this when you get a chance?

[LeeTL1220]

@samuelklee This looks pretty straight-forward.