The debug command line argument is now passed correctly in Haplotype caller -- fixed issue #4943 #5455
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…t 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.
.../java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
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...main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet.java
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davidbenjamin
requested changes
Nov 29, 2018
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Closes #4943 for github |
Codecov Report
@@ 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
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Finished the requests of @davidbenjamin |
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java
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…usly, I set those after initialization in Mutect2Engine and HaplotypeCallerEngine, and now I do it at initialization.
davidbenjamin
approved these changes
Nov 30, 2018
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@MartonKN Looks good! |
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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.