Rev picard, sam-jdk, tribble, and variant jars to 1.104.1628

-update VariantFiltration to work with new Lazy wrapper around the
 JexlEngine in VariantContextUtils

public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java

@@ -230,7 +230,7 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
         filterExps = VariantContextUtils.initializeMatchExps(FILTER_NAMES, FILTER_EXPS);
         genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
 
-        VariantContextUtils.engine.setSilent(true);
+        VariantContextUtils.engine.get().setSilent(true);
 
         initializeVcfWriter();
     }

settings/repository/net.sf/picard-1.102.1595.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.102.1595" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.104.1628.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.104.1628" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.102.1595.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.102.1595" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.104.1628.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.104.1628" status="release" />
+</ivy-module>

settings/repository/org.broad/tribble-1.104.1628.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.102.1595" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.104.1628" status="integration" />
 </ivy-module>

settings/repository/org.broadinstitute/variant-1.104.1628.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.102.1595" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.104.1628" status="integration" />
 </ivy-module>