diff --git a/build.xml b/build.xml
index fe1723587..b9fdd5dbe 100644
--- a/build.xml
+++ b/build.xml
@@ -69,8 +69,6 @@
 
     <property environment="env"/>
 
-    <property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
-
     <patternset id="java.source.pattern">
         <include name="${java.public.source.dir}/**/*.java" />
         <include name="${java.private.source.dir}/**/*.java" if="include.private" />
@@ -146,11 +144,7 @@
         <property name="init.resolve.done" value="true"/>
     </target>
 
-    <target name="init.gridengine" depends="init" if="include.gridengine">
-        <copy todir="lib" file="${drmaa.jar}"/>
-    </target>
-
-    <target name="resolve" depends="init.resolve,init,init.gridengine"
+    <target name="resolve" depends="init.resolve,init"
             description="locate and download library dependencies">
         <property name="ivy.conf" value="default"/>
       <ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
@@ -178,13 +172,23 @@
         <property name="build.version" value="${git.describe.output}" />
     </target>
     
-    <target name="untagged.build.version" depends="git.describe" unless="git.describe.succeeded">
-      <exec executable="git" outputproperty="build.version" failonerror="true">
+    <target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
+      <exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
         <arg line="rev-parse HEAD" />
       </exec>
+      <condition property="git.rev-parse.succeeded">
+        <equals arg1="${git.rev-parse.exit.value}" arg2="0" />
+      </condition>
     </target>
     
-    <target name="generate.build.version" depends="tagged.build.version, untagged.build.version" />
+    <target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
+        <property name="build.version" value="${git.rev-parse.output}" />
+    </target>
+    
+    <target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
+        <!-- Set build.version to exported if no other value has been set -->
+        <property name="build.version" value="exported" />
+    </target>
 
     <!-- define some key locations that might change based on how the build is run -->
     <target name="init" depends="generate.build.version">
@@ -214,12 +218,6 @@
             </or>
         </condition>
 
-        <!-- Include Grid Engine in the compile if SGE_ROOT is available. -->
-        <!-- Based off of http://wikis.sun.com/display/GridEngine/Automating+Grid+Engine+Functions+Through+DRMAA -->
-        <condition property="include.gridengine">
-            <available file="${drmaa.jar}"/>
-        </condition>
-
         <echo message="GATK build      : ${gatk.target}"/>
         <echo message="Scala build     : ${scala.target}"/>
       <echo message="source revision : ${build.version}"/>
@@ -357,7 +355,6 @@
             <src path="${scala.public.source.dir}" />
             <src path="${queue-extensions.source.dir}" />
             <include name="**/*.scala"/>
-            <exclude name="**/gridengine/**" unless="include.gridengine" />
         </scalac>    
     </target>
     
@@ -374,7 +371,6 @@
         <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
             <src path="${scala.private.source.dir}" />
             <include name="**/*.scala"/>
-            <exclude name="**/gridengine/**" unless="include.gridengine" />
         </scalac>       
     </target>
 
@@ -464,7 +460,7 @@
               <exclude name="**/utils/variantcontext/**/*.class"/>
             </fileset>
             <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/datasources/**/*.class"/>
+            <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
@@ -682,7 +678,6 @@
 	        <src path="${scala.public.test.sources}" />
 	        <src path="${scala.private.test.sources}" />
             <include name="**/*.scala"/>
-            <exclude name="**/gridengine/**" unless="include.gridengine" />
             <classpath>
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
diff --git a/ivy.xml b/ivy.xml
index c2a6c4ccd..10e4ee570 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -48,6 +48,9 @@
     <!-- Dependencies for amazon.com S3 support -->
     <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/>
 
+    <!-- Dependencies for GridEngine -->
+    <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
+
     <!-- Scala dependancies -->
     <dependency org="org.scala-lang" name="scala-compiler" rev="2.8.1"/>
     <dependency org="org.scala-lang" name="scala-library" rev="2.8.1"/>
diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
index 3cf43c15a..f8e298d88 100755
--- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
@@ -61,7 +61,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
     @Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript. For Broad users this is maybe /broad/tools/apps/R-2.6.0/bin/Rscript", required = false)
     private String PATH_TO_RSCRIPT = "Rscript";
     @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required = false)
-    private String PATH_TO_RESOURCES = "R/";
+    private String PATH_TO_RESOURCES = "public/R/";
     @Argument(fullName = "ignoreQ", shortName = "ignoreQ", doc = "Ignore bases with reported quality less than this number.", required = false)
     private int IGNORE_QSCORES_LESS_THAN = 5;
     @Argument(fullName = "numRG", shortName = "numRG", doc = "Only process N read groups. Default value: -1 (process all read groups)", required = false)            
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 1045ca371..055eb0b97 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -92,25 +92,31 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false)
     public double INDEL_HETEROZYGOSITY = 1.0/8000;
 
+    @Hidden
     @Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty", required = false)
     public double INDEL_GAP_CONTINUATION_PENALTY = 10.0;
 
+    @Hidden
     @Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty", required = false)
     public double INDEL_GAP_OPEN_PENALTY = 45.0;
 
+    @Hidden
     @Argument(fullName = "indelHaplotypeSize", shortName = "indelHSize", doc = "Indel haplotype size", required = false)
     public int INDEL_HAPLOTYPE_SIZE = 80;
+    @Hidden
     @Argument(fullName = "doContextDependentGapPenalties", shortName = "doCDP", doc = "Vary gap penalties by context", required = false)
      public boolean DO_CONTEXT_DEPENDENT_PENALTIES = true;
     //gdebug+
-    @Hidden
     // experimental arguments, NOT TO BE USED BY ANYONE WHOSE INITIALS AREN'T GDA!!!
+    @Hidden
     @Argument(fullName = "getGapPenaltiesFromData", shortName = "dataGP", doc = "Vary gap penalties by context - EXPERIMENTAL, DO NO USE", required = false)
     public boolean GET_GAP_PENALTIES_FROM_DATA = false;
 
+    @Hidden
     @Argument(fullName="indel_recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE")
     public File INDEL_RECAL_FILE = new File("indel.recal_data.csv");
 
+    @Hidden
     @Argument(fullName = "indelDebug", shortName = "indelDebug", doc = "Output indel debug info", required = false)
     public boolean OUTPUT_DEBUG_INDEL_INFO = false;
     @Hidden
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index aebb0e3eb..df1f4f908 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -5,6 +5,7 @@ import net.sf.samtools.*;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
@@ -113,9 +114,10 @@ public class ConstrainedMateFixingManager {
     HashMap<String, SAMRecordHashObject> forMateMatching = new HashMap<String, SAMRecordHashObject>();
     TreeSet<SAMRecord> waitingReads = new TreeSet<SAMRecord>(comparer);
 
-    private <T> T remove(TreeSet<T> treeSet) {
-        final T first = treeSet.first();
-        treeSet.remove(first);
+    private SAMRecord remove(TreeSet<SAMRecord> treeSet) {
+        final SAMRecord first = treeSet.first();
+        if ( !treeSet.remove(first) )
+            throw new UserException("Error caching SAM record " + first.getReadName() + ", which is usually caused by malformed SAM/BAM files in which multiple identical copies of a read are present.");
         return first;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 02d850211..d4e07dccf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2011 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index a09a30145..1f622afc8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import Jama.Matrix;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
index 0b2edfd10..d077af78e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import Jama.Matrix;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
index 9bbcf395a..6c1a7ddbc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
index fbee64fe2..64fe36637 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2011 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
index 08388db21..19c6d501b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 2914385a4..5deb5d8c2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -1,8 +1,32 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantQualityScore;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index f83e9b2f0..357bbaa24 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import cern.jet.random.Normal;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
index 04a5a9d3e..eb9e98fcb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index b903d20af..2c51f02d6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -88,7 +88,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     @Argument(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false)
     private String RSCRIPT_FILE = null;
     @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required=false)
-    private String PATH_TO_RESOURCES = "R/";
+    private String PATH_TO_RESOURCES = "public/R/";
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots", required=false)
     private double TS_FILTER_LEVEL = 99.0;
 
@@ -118,6 +118,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     //---------------------------------------------------------------------------------------------------------------
 
     public void initialize() {
+        if( !PATH_TO_RESOURCES.endsWith("/") ) { PATH_TO_RESOURCES = PATH_TO_RESOURCES + "/"; }
         dataManager = new VariantDataManager( new ArrayList<String>(Arrays.asList(USE_ANNOTATIONS)), VRAC );
 
         if( IGNORE_INPUT_FILTERS != null ) {
@@ -228,19 +229,23 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     public void onTraversalDone( final ExpandingArrayList<VariantDatum> reduceSum ) {
         dataManager.setData( reduceSum );
         dataManager.normalizeData(); // Each data point is now (x - mean) / standard deviation
+
+        // Generate the positive model using the training data and evaluate each variant
         final GaussianMixtureModel goodModel = engine.generateModel( dataManager.getTrainingData() );
         engine.evaluateData( dataManager.getData(), goodModel, false );
+
+        // Generate the negative model using the worst performing data and evaluate each variant contrastively
         final GaussianMixtureModel badModel = engine.generateModel( dataManager.selectWorstVariants( VRAC.PERCENT_BAD_VARIANTS, VRAC.MIN_NUM_BAD_VARIANTS ) );
         engine.evaluateData( dataManager.getData(), badModel, true );
         engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel );
 
-        final ExpandingArrayList<VariantDatum> randomData = dataManager.getRandomDataForPlotting( 6000 );
-
+        // Find the VQSLOD cutoff values which correspond to the various tranches of calls requested by the user
         final int nCallsAtTruth = TrancheManager.countCallsAtTruth( dataManager.getData(), Double.NEGATIVE_INFINITY );
         final TrancheManager.SelectionMetric metric = new TrancheManager.TruthSensitivityMetric( nCallsAtTruth );
         final List<Tranche> tranches = TrancheManager.findTranches( dataManager.getData(), TS_TRANCHES, metric );
         tranchesStream.print(Tranche.tranchesString( tranches ));
 
+        // Find the filtering lodCutoff for display on the model PDFs. Red variants are those which were below the cutoff and filtered out of the final callset.
         double lodCutoff = 0.0;
         for( final Tranche tranche : tranches ) {
             if( MathUtils.compareDoubles(tranche.ts, TS_FILTER_LEVEL, 0.0001)==0 ) {
@@ -252,7 +257,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         dataManager.writeOutRecalibrationTable( RECAL_FILE );
         if( RSCRIPT_FILE != null ) {
             logger.info( "Writing out visualization Rscript file...");
-            createVisualizationScript( randomData, goodModel, badModel, lodCutoff );
+            createVisualizationScript( dataManager.getRandomDataForPlotting( 6000 ), goodModel, badModel, lodCutoff );
         }
 
         // Execute Rscript command to create the tranche plot
@@ -278,6 +283,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         } catch( FileNotFoundException e ) {
             throw new UserException.CouldNotCreateOutputFile(RSCRIPT_FILE, "", e);
         }
+
+        // We make extensive use of the ggplot2 library: http://had.co.nz/ggplot2/
         stream.println("library(ggplot2)");
 
         createArrangeFunction( stream );
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index e177cebab..f597fb128 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.broadinstitute.sting.commandline.Argument;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
index 81e4d190c..52b48ff08 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
@@ -1,3 +1,28 @@
+/*
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 3d375aba2..5787b591f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1343,6 +1343,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return (int)stop;
     }
 
+    private boolean hasSymbolicAlleles() {
+        for (Allele a: getAlleles()) {
+            if (a.isSymbolic()) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
         Allele refAllele = inputVC.getReference();
 
@@ -1352,7 +1361,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
         // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
         long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
-        if (refAllele.length() == locLength)
+        if (inputVC.hasSymbolicAlleles())
+            padVC = true;
+        else if (refAllele.length() == locLength)
             padVC = false;
         else if (refAllele.length() == locLength-1)
             padVC = true;
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index d71c6ae5d..a961beca1 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -19,10 +19,7 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
 class MethodsDevelopmentCallingPipeline extends QScript {
   qscript =>
 
-  @Argument(shortName="gatk", doc="gatk jar file", required=true)
-  var gatkJarFile: File = _
-
-  @Argument(shortName="outputDir", doc="output directory", required=true)
+  @Argument(shortName="outputDir", doc="output directory", required=false)
   var outputDir: String = "./"
 
   @Argument(shortName="skipCalling", doc="skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)
@@ -185,7 +182,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
 
   trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
     logging_level = "INFO";
-    jarFile = gatkJarFile;
     memoryLimit = 4;
     phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3
   }
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
index 1e47fa847..2c8fc388f 100644
--- a/settings/ivysettings.xml
+++ b/settings/ivysettings.xml
@@ -25,5 +25,6 @@
     <module organisation="javax.activation" resolver="java.net" />
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
+    <module organisation="net.sf.gridscheduler" resolver="projects" />
   </modules>
 </ivysettings>
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar
new file mode 100644
index 000000000..dc77c7d33
Binary files /dev/null and b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar differ
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar
new file mode 100644
index 000000000..f267be4b5
Binary files /dev/null and b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar differ
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
new file mode 100644
index 000000000..c6a8da052
--- /dev/null
+++ b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf.gridscheduler" module="drmaa" revision="6.2u5p2" status="release" />
+</ivy-module>