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Add DeprecatedFeature annotation. #8100
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@@ -2,6 +2,7 @@ | |
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import org.broadinstitute.barclay.argparser.Advanced; | ||
import org.broadinstitute.barclay.argparser.Argument; | ||
import org.broadinstitute.barclay.argparser.DeprecatedFeature; | ||
import org.broadinstitute.barclay.argparser.Hidden; | ||
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; | ||
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@@ -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 | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. This has been deprecated since 3.3... maybe we can remove it. There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Can we put the reason in the description? |
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@Argument(fullName= RECOVER_DANGLING_HEADS_LONG_NAME, doc="This argument is deprecated since version 3.3", optional = true) | ||
public boolean DEPRECATED_RecoverDanglingHeads = false; | ||
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import org.broadinstitute.barclay.argparser.Advanced; | ||
import org.broadinstitute.barclay.argparser.Argument; | ||
import org.broadinstitute.barclay.argparser.ArgumentCollection; | ||
import org.broadinstitute.barclay.argparser.DeprecatedFeature; | ||
import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions; | ||
import org.broadinstitute.hellbender.engine.FeatureInput; | ||
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection; | ||
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@@ -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 | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Should we move the reason into here? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Sure. Done. |
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@Argument(fullName = TUMOR_SAMPLE_LONG_NAME, shortName = TUMOR_SAMPLE_SHORT_NAME, doc = "BAM sample name of tumor. May be URL-encoded as output by GetSampleName with -encode argument.", optional = true) | ||
protected String tumorSample = null; | ||
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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.