From 1fe815511151ceb9f35f89fd4ab7bacf717e6e41 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 May 2009 21:47:34 +0000
Subject: [PATCH] Some critical fixes for cases where argument values directly
 abut argument names and for arguments with missing short names.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@610 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/cmdLine/ArgumentDefinitions.java               | 2 +-
 .../org/broadinstitute/sting/utils/cmdLine/HelpFormatter.java  | 3 ---
 .../org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java  | 2 +-
 3 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
index 542410868..ca473f422 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinitions.java
@@ -50,7 +50,7 @@ class ArgumentDefinitions implements Iterable<ArgumentDefinition> {
                 throw new IllegalArgumentException( "Argument cannot have 0-length fullname." );
             if( hasArgumentDefinition( definition.fullName, FullNameDefinitionMatcher ) )
                 throw new StingException("Duplicate definition of argument with full name: " + definition.fullName);
-            if( hasArgumentDefinition( definition.shortName, ShortNameDefinitionMatcher ) )
+            if( definition.shortName != null && hasArgumentDefinition( definition.shortName, ShortNameDefinitionMatcher ) )
                 throw new StingException("Duplicate definition of argument with short name: " + definition.shortName);
 
             argumentDefinitions.add( definition );
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/HelpFormatter.java b/java/src/org/broadinstitute/sting/utils/cmdLine/HelpFormatter.java
index 8a6607543..f440fc4c6 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/HelpFormatter.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/HelpFormatter.java
@@ -3,15 +3,12 @@ package org.broadinstitute.sting.utils.cmdLine;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Formatter;
-import java.util.Locale;
-import java.util.Formattable;
 import java.util.List;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.HashMap;
 import java.util.Comparator;
-import java.util.Set;
 import java.util.TreeSet;
 import java.util.SortedSet;
 import java.util.Collection;
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
index 8991e516c..36c82b53d 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
@@ -60,7 +60,7 @@ public class ParsingEngine {
 
     public ParsingEngine() {
         parsingMethods.add( new ParsingMethod(Pattern.compile("\\s*--([\\w\\.]+)\\s*"), ArgumentDefinitions.FullNameDefinitionMatcher) );
-        parsingMethods.add( new ParsingMethod(Pattern.compile("\\s*-([\\w\\.])([\\w\\.]*)\\s*"),
+        parsingMethods.add( new ParsingMethod(Pattern.compile("\\s*-([\\w\\.])([\\w\\.\\/:\\-]*)\\s*"),
                             ArgumentDefinitions.ShortNameDefinitionMatcher,
                             ArgumentDefinitions.ShortNameAliasProvider) );
     }