From 93f7e632bd2febd5f8af2e846bf054893997dee0 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Thu, 6 Oct 2011 10:07:46 -0400
Subject: [PATCH 2/3] Minor fix/enhancement for VariantEval: if a vcf has
 symbolic alleles, program would crash ungracefully - now we'll just skip
 record without processing. This is a big issue since we can't process 1000G
 integration files with code as is.

---
 .../gatk/walkers/varianteval/evaluators/CountVariants.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index 72058ba7b..e83434037 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -130,6 +130,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nVariantLoci++;
                     nMixed++;
                     break;
+                case SYMBOLIC:
+                    // ignore symbolic alleles, but don't fail
+                    // todo - consistent way of treating symbolic alleles thgoughout codebase?
+                    break;
                 default:
                     throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
             }

From efca1fdfd8a5e6cf25062911f142bb1bfcabea9b Mon Sep 17 00:00:00 2001
From: Matt Hanna <hanna@broadinstitute.org>
Date: Thu, 6 Oct 2011 10:08:48 -0400
Subject: [PATCH 3/3] Revert change until I figure out how to use
 classfileset/rootfileset with a vanilla ant install.

This reverts commit 4c9022872beec8dc0700a1320a267e3603c8212d.
---
 build.xml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/build.xml b/build.xml
index 1e5aaf644..1f26e7b7a 100644
--- a/build.xml
+++ b/build.xml
@@ -545,10 +545,12 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-	    <classfileset dir="${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>
+            <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>
         </jar>
     </target>