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Force isRequired() to be false for @Deprecated args. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4092 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-08-23 23:50:30 +00:00
parent 5d6a6420a9
commit 691333f75c
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -148,7 +148,7 @@ public abstract class ArgumentTypeDescriptor {
ArgumentDefinition.getFullName(argumentAnnotation, source.field.getName()),
ArgumentDefinition.getShortName(argumentAnnotation),
ArgumentDefinition.getDoc(argumentAnnotation),
source.isRequired() && !source.overridesDefault() && !source.isFlag(),
source.isRequired() && !source.overridesDefault() && !source.isFlag() && !source.isDeprecated(),
source.isFlag(),
source.isMultiValued(),
source.isHidden(),

2
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -72,7 +72,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Output(required=false, doc="Output bam")
protected String writerFilename = null;
@Argument(fullName="output",shortName="O",doc="Please use --out instead",required=false)
@Argument(fullName="output",shortName="O",doc="Please use --out instead")
@Deprecated
protected String oldOArg;