Populating the DB SNP validation status field properly #5046
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…hat is left is one more integration test.
Codecov Report
@@ Coverage Diff @@
## master #5046 +/- ##
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- Coverage 86.382% 85.374% -1.008%
- Complexity 28674 28718 +44
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Files 1785 1791 +6
Lines 132713 134756 +2043
Branches 14766 15131 +365
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+ Hits 114640 115047 +407
- Misses 12746 14348 +1602
- Partials 5327 5361 +34
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@jonn-smith Looks like the travis failures are transient... |
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@jonn-smith Can you review this? |
jonn-smith
requested changes
Aug 15, 2018
| if (doesRegion1ContainAnnotation && doesRegion2ContainAnnotation) { | ||
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| // Both regions contain an annotation and presumably these are of different values. | ||
| return conflictFunction.apply(funcotation1.getField(fieldName), |
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Should we do anything differently if the values of the funcotations are the same?
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It already does nothing. Just takes the value. I think this is the correct behavior. No action.
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| import static org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants.MAF_RENDERING_DATASOURCE_DUMMY_NAME; | ||
| import static org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants.*; |
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Can you remove the static import and reference the constants by full name instead?
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@jonn-smith Can I merge if the tests pass? |
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Travis error is transient. |
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dbSNP_Val_Statusis incorrect when rendering MAF files. #4985