Add DeprecatedFeature annotation. #8100
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Github actions tests reported job failures from actions build 3527272492
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Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #8100 +/- ##
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+ Coverage 84.069% 86.604% +2.535%
- Complexity 37456 38940 +1484
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Files 2335 2335
Lines 182679 182680 +1
Branches 20052 20052
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+ Hits 153577 158209 +4632
+ Misses 22059 17433 -4626
+ Partials 7043 7038 -5
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@cmnbroad Minor comments.
It might be nice to replace the (Deprecated) mark in the html with something more like the little bubbles for the input type so it stands out a bit more. (even if it's in its own dedicated section.)
| @@ -32,7 +33,7 @@ public class HaplotypeCallerReadThreadingAssemblerArgumentCollection extends Rea | |||
| /** | |||
| * As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior. See GATK 3.3 release notes for more details. | |||
| */ | |||
| @Deprecated | |||
| @DeprecatedFeature | |||
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This has been deprecated since 3.3... maybe we can remove it.
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Can we put the reason in the description?
| @@ -115,7 +116,7 @@ public ReadThreadingAssembler createReadThreadingAssembler(){ | |||
| public File f1r2TarGz; | |||
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| // As of GATK 4.1, any sample not specified as the normal is considered a tumor sample | |||
| @Deprecated | |||
| @DeprecatedFeature | |||
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Should we move the reason into here?
| @@ -61,7 +62,7 @@ public GenotypeCalculationArgumentCollection clone() { | |||
| /** | |||
| * As of version 4.1.0.0, this argument is no longer needed because the new qual score is now on by default. See GATK 3.3 release notes for more details. | |||
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Does javadoc on arguments get output in our docs at all?
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Yes, it gets included in the full text description.
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@cmnbroad Are we waiting on something to merge this? 👍 from me. |
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Upgrades Barclay to 4.1.0. Adds an
@DeprecatedFeatureannotation that can be applied to any@DocumentedFeatureor@Argument, and updates the handful of such features that are already tagged with the standard Java annotation@Deprecatedto use the new annotation. Mutually exclusive with@Betaand@Experimental.The output for
--use-new-qual-calculator: