From 21091b98398c3d65e06ea9034b53c6d08a8a41cd Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 19 Aug 2009 19:42:39 +0000
Subject: [PATCH] Fix for invalid format error when outputting BAM files.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1438 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/cmdLine/ArgumentTypeDescriptor.java           | 4 ++--
 .../org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
index a755e1b1d..7b29a6ba1 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java
@@ -352,8 +352,8 @@ class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                                                                            COMPRESSION_SHORTNAME,
                                                                            "Compression level to use for writing BAM files",
                                                                            false,
-                                                                           "",
-                                                                           "" );
+                                                                           null,
+                                                                           null );
 
         return Arrays.asList( writerDefinition, compressionDefinition );
     }
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
index a252b08a8..b4fe1c164 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
@@ -258,9 +258,6 @@ public class ParsingEngine {
         if( argumentMatches.size() == 0 )
             return;
 
-        if( argumentMatches.size() > 1 )
-            throw new StingException("Too many values matched argument: " + source.field.getName());
-
         if( source.clazz.isAssignableFrom(target.getClass()) ) {
             Object value = source.parse( source, target, argumentMatches.toArray(new ArgumentMatch[0]) );
             if( clp == null || !clp.intercept(source, target, value) )