From 3841635fcb4d711df818b6d62df722ef70cddffc Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Fri, 16 Aug 2013 13:06:41 -0400
Subject: [PATCH] Changed 'depreciated' to the more correct 'deprecated'

---
 .../sting/utils/help/GenericDocumentationHandler.java       | 6 +++---
 settings/helpTemplates/generic.template.html                | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 01221cf27..f124410e0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -197,7 +197,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         if (argumentSource.isRequired()) return "required";
         else if (argumentSource.isAdvanced()) return "advanced";
         else if (argumentSource.isHidden()) return "hidden";
-        else if (argumentSource.isDeprecated()) return "depreciated";
+        else if (argumentSource.isDeprecated()) return "deprecated";
         else return "optional";
     }
 
@@ -242,7 +242,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         args.put("optional", new ArrayList<Map<String, Object>>());
         args.put("advanced", new ArrayList<Map<String, Object>>());
         args.put("hidden", new ArrayList<Map<String, Object>>());
-        args.put("depreciated", new ArrayList<Map<String, Object>>());
+        args.put("deprecated", new ArrayList<Map<String, Object>>());
         return args;
     }
 
@@ -843,7 +843,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         // general attributes
         List<String> attributes = new ArrayList<String>();
         if (def.required) attributes.add("required");
-        if (source.isDeprecated()) attributes.add("depreciated");
+        if (source.isDeprecated()) attributes.add("deprecated");
         if (attributes.size() > 0)
             root.put("attributes", Utils.join(", ", attributes));
 
diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index ea9fa2d72..589eed927 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -239,7 +239,7 @@
 					<@argumentlist name="Optional" myargs=arguments.optional/>
 					<@argumentlist name="Advanced" myargs=arguments.advanced/>
 					<@argumentlist name="Hidden" myargs=arguments.hidden/>
-					<@argumentlist name="Depreciated" myargs=arguments.depreciated/>
+					<@argumentlist name="Deprecated" myargs=arguments.deprecated/>
 					</tbody>
 				</table>
 			</#if>