The debug command line argument is now passed correctly in Haplotype caller -- fixed issue #4943

[MartonKN]

The debug variable of AsseemblyResultSet wasn't set anywhere, and therefore the command line argument debug didn't propagate to the function buildEventMapsForHaplotypes in EventMap.java. I added the function setDebug to AssemblyResultSet, and set its value in HaplotypeCallerEngine.

[davidbenjamin]

@MartonKN don't forget to put in: closes #4943 for github.

[davidbenjamin]

Back to @MartonKN.

[MartonKN]

Closes #4943 for github

[codecov-io]

Codecov Report

Merging #5455 into master will decrease coverage by 0.02%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##              master     #5455      +/-   ##
==============================================
- Coverage     87.004%   86.984%   -0.02%     
- Complexity     31190     31202      +12     
==============================================
  Files           1908      1909       +1     
  Lines         144073    144198     +125     
  Branches       15937     15951      +14     
==============================================
+ Hits          125349    125429      +80     
- Misses         12963     13000      +37     
- Partials        5761      5769       +8

Impacted Files	Coverage Δ	Complexity Δ
...llbender/engine/filters/CountingVariantFilter.java	100% <ø> (ø)	18 <0> (ø)	⬇️
...walkers/haplotypecaller/HaplotypeCallerEngine.java	78.125% <ø> (ø)	74 <0> (ø)	⬇️
...hellbender/tools/walkers/mutect/Mutect2Engine.java	89.881% <ø> (ø)	63 <0> (ø)	⬇️
...kers/haplotypecaller/AssemblyBasedCallerUtils.java	76.744% <ø> (+0.182%)	35 <0> (ø)	⬇️
...ols/walkers/haplotypecaller/AssemblyResultSet.java	75.74% <100%> (+0.291%)	45 <1> (+1)	⬆️
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...ataSources/xsv/LocatableXsvFuncotationFactory.java	79.452% <0%> (-3.647%)	21% <0%> (-1%)
...oadinstitute/hellbender/engine/FeatureManager.java	84.071% <0%> (-3.085%)	49% <0%> (ø)
...tils/annotatedinterval/AnnotatedIntervalCodec.java	77.778% <0%> (-1.533%)	18% <0%> (ø)
...dataSources/gencode/GencodeFuncotationFactory.java	86.536% <0%> (-1.494%)	230% <0%> (+1%)
... and 14 more

[MartonKN]

Finished the requests of @davidbenjamin

[davidbenjamin]

@MartonKN Looks good!