From dd780dba5fa5b07591bda94b58ac505e9131ca89 Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Wed, 5 Oct 2011 18:25:26 -0400
Subject: [PATCH 1/2] Rather than just picking a few classes to be the roots of
 the vcf jar and including all dependencies, use the entire codecs.vcf and
 variantcontext packages as roots.

Fix for my fix for Jim Robinson.
---
 build.xml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/build.xml b/build.xml
index 1f26e7b7a..1e5aaf644 100644
--- a/build.xml
+++ b/build.xml
@@ -545,12 +545,10 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-            <fileset dir="${java.classes}">
-              <include name="**/utils/codecs/**/*.class"/>
-              <include name="**/utils/variantcontext/**/*.class"/>
-              <include name="org/broadinstitute/sting/utils/exceptions/**"/>
-	      <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
-            </fileset>
+	    <classfileset dir="${java.classes}">
+	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/codecs/vcf/**/*.class" />
+	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/variantcontext/**/*.class" />
+	    </classfileset>
         </jar>
     </target>
 

From 6d6149b9a2ecdb6c401460ac10db6ee90de27ede Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 5 Oct 2011 18:30:40 -0400
Subject: [PATCH 2/2] Updated gsalib gsa.read.gatkreport to return all reports,
 even those beginning with '.'. In PreQC using geom_blank() so
 MEDIAN_INSERT_SIZE plot doesn't crash on facet_grid(scales='free') when data
 doesn't contain points for 'RF' or 'TANDEM'.

---
 public/R/src/gsalib/R/gsa.read.gatkreport.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/R/src/gsalib/R/gsa.read.gatkreport.R b/public/R/src/gsalib/R/gsa.read.gatkreport.R
index 011b5240d..46bbf7eda 100644
--- a/public/R/src/gsalib/R/gsa.read.gatkreport.R
+++ b/public/R/src/gsalib/R/gsa.read.gatkreport.R
@@ -99,5 +99,5 @@ gsa.read.gatkreport <- function(filename) {
         .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
     }
 
-    gatkreport = as.list(tableEnv);
+    gatkreport = as.list(tableEnv, all.names=TRUE);
 }