From 691333f75c988a715d05facb902258e9f45ee71e Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 Aug 2010 23:50:30 +0000
Subject: [PATCH] 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
---
 .../sting/commandline/ArgumentTypeDescriptor.java               | 2 +-
 .../sting/gatk/walkers/indels/IndelRealigner.java               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 893709a42..acbef061e 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -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(),
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index c1855d7da..eb8e0485e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -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;