kebab case some arguments in LocusWalker and Spark walkers #5770
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Thanks @davidbenjamin! Couple more in AssemblyRegionReadShardArgumentCollection? |
Codecov Report
@@ Coverage Diff @@
## master #5770 +/- ##
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+ Coverage 86.982% 86.984% +0.003%
- Complexity 31861 31863 +2
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Files 1943 1943
Lines 146770 146768 -2
Branches 16223 16223
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+ Hits 127663 127665 +2
+ Misses 13194 13189 -5
- Partials 5913 5914 +1
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@samuelklee They're in this PR (that's the #5478 part). |
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Oops, duh, so they are---didn't realize it from the title alone and misread the diff between this and another one of my branches! |
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@davidbenjamin One comment. Good to merge when that is addressed! Thanks for doing this!
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| */ | |||
| public abstract class LocusWalker extends GATKTool { | |||
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| @Argument(fullName = "maxDepthPerSample", shortName = "maxDepthPerSample", doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true) | |||
| @Argument(fullName = "max-depth-per-sample", shortName = "max-depth-per-sample", doc = "Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.", optional = true) | |||
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There are two error messages that refer to the old maxDepthPerSample one in LocusWalker.getDownsamplingInfo() and the other in LocusWalkerSpark. Could you extract a constant from this and have all three locations use it?
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Also @lbergelson please disregard that second review request! Man am I looking foolish on this branch. |
Closes #5479. Closes #5478.
@lbergelson here you go.