diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 0aae62c5c..6f65132c2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval;
 
+import org.apache.log4j.Logger;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.vcf.VCFConstants;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -17,21 +17,14 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.AnalysisModuleScanner;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.report.utils.TableType;
@@ -43,7 +36,7 @@ import java.lang.reflect.Field;
 import java.util.*;
 
 /**
- * General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ts/Tv ratios, and a lot more)
+ * General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
  */
 @Reference(window=@Window(start=-50, stop=50))
 public class VariantEvalWalker extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
@@ -99,7 +92,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     private String TRANCHE_FILENAME = null;
 
     // Variables
-    private Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions = new TreeSet<VariantContextUtils.JexlVCMatchExp>();
+    private Set<SortableJexlVCMatchExp> jexlExpressions = new TreeSet<SortableJexlVCMatchExp>();
     private Set<String> compNames = new TreeSet<String>();
     private Set<String> knownNames = new TreeSet<String>();
     private Set<String> evalNames = new TreeSet<String>();
@@ -118,240 +111,17 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     private GATKReport report = null;
 
     // Public constants
-    public static String ALL_SAMPLE_NAME = "all";
+    private static String ALL_SAMPLE_NAME = "all";
 
-    /**
-     * List all of the available evaluation modules, then exit successfully
-     */
-    private void listModulesAndExit() {
-        List<Class<? extends VariantStratifier>> vsClasses = new PluginManager<VariantStratifier>( VariantStratifier.class ).getPlugins();
-        List<Class<? extends VariantEvaluator>> veClasses = new PluginManager<VariantEvaluator>( VariantEvaluator.class ).getPlugins();
-
-        logger.info("Available stratification modules:");
-        logger.info("(Standard modules are starred)");
-        for (Class<? extends VariantStratifier> vsClass : vsClasses) {
-            logger.info("\t" + vsClass.getSimpleName() + (RequiredStratification.class.isAssignableFrom(vsClass) || StandardStratification.class.isAssignableFrom(vsClass) ? "*" : ""));
-        }
-        logger.info("");
-
-        logger.info("Available evaluation modules:");
-        logger.info("(Standard modules are starred)");
-        for (Class<? extends VariantEvaluator> veClass : veClasses) {
-            logger.info("\t" + veClass.getSimpleName() + (StandardEval.class.isAssignableFrom(veClass) ? "*" : ""));
-        }
-        logger.info("");
-
-        System.exit(0);
-    }
-
-    /**
-     * Initialize required, standard and user-specified stratification objects
-     *
-     * @param noStandardStrats  don't use the standard stratifications
-     * @param modulesToUse      the list of stratification modules to use
-     * @return  set of stratifications to use
-     */
-    private TreeSet<VariantStratifier> initializeStratificationObjects(boolean noStandardStrats, String[] modulesToUse) {
-        TreeSet<VariantStratifier> strats = new TreeSet<VariantStratifier>();
-        Set<String> stratsToUse = new HashSet<String>();
-
-        // Create a map for all stratification modules for easy lookup.
-        HashMap<String, Class<? extends VariantStratifier>> classMap = new HashMap<String, Class<? extends VariantStratifier>>();
-        for ( Class<? extends VariantStratifier> c : new PluginManager<VariantStratifier>( VariantStratifier.class ).getPlugins() ) {
-            classMap.put(c.getSimpleName(), c);
-        }
-
-        // We must use all required stratification modules.
-        for ( Class<? extends RequiredStratification> reqClass : new PluginManager<RequiredStratification>( RequiredStratification.class ).getPlugins() ) {
-            if ( classMap.containsKey(reqClass.getSimpleName()) ) {
-                stratsToUse.add(reqClass.getSimpleName());
-            }
-        }
-
-        // By default, use standard stratification modules.
-        if ( !noStandardStrats ) {
-            for ( Class<? extends StandardStratification> stdClass : new PluginManager<StandardStratification>( StandardStratification.class ).getPlugins() ) {
-                if ( classMap.containsKey(stdClass.getSimpleName()) ) {
-                    stratsToUse.add(stdClass.getSimpleName());
-                }
-            }
-        }
-
-        // Now add the user-selected modules
-        stratsToUse.addAll(Arrays.asList(modulesToUse));
-
-        // Instantiate the stratifications
-        for ( String module : stratsToUse ) {
-            if ( !classMap.containsKey(module) ) {
-                throw new UserException.CommandLineException("Module " + module + " could not be found; please check that you have specified the class name correctly");
-            }
-
-            if ( classMap.containsKey(module) ) {
-                Class<? extends VariantStratifier> c = classMap.get(module);
-
-                try {
-                    VariantStratifier vs = c.newInstance();
-                    vs.initialize(jexlExpressions, compNames, knownNames, evalNames, sampleNamesForStratification);
-
-                    strats.add(vs);
-                } catch (InstantiationException e) {
-                    throw new StingException("Unable to instantiate stratification module '" + c.getSimpleName() + "'");
-                } catch (IllegalAccessException e) {
-                    throw new StingException("Illegal access error when trying to instantiate stratification module '" + c.getSimpleName() + "'");
-                }
-            }
-        }
-
-        return strats;
-    }
-
-    /**
-     * Initialize required, standard and user-specified evaluation objects
-     *
-     * @param noStandardEvals  don't use the standard evaluations
-     * @param modulesToUse     the list of evaluation modules to use
-     * @return  set of evaluations to use
-     */
-    private Set<Class<? extends VariantEvaluator>> initializeEvaluationObjects(boolean noStandardEvals, String[] modulesToUse) {
-        Set<Class<? extends VariantEvaluator>> evals = new HashSet<Class<? extends VariantEvaluator>>();
-
-        // Create a map for all eval modules for easy lookup.
-        HashMap<String, Class<? extends VariantEvaluator>> classMap = new HashMap<String, Class<? extends VariantEvaluator>>();
-        for ( Class<? extends VariantEvaluator> c : new PluginManager<VariantEvaluator>( VariantEvaluator.class ).getPlugins() ) {
-            classMap.put(c.getSimpleName(), c);
-        }
-
-        // By default, use standard eval modules.
-        if ( !noStandardEvals ) {
-            for ( Class<? extends StandardEval> stdClass : new PluginManager<StandardEval>( StandardEval.class ).getPlugins() ) {
-                if ( classMap.containsKey(stdClass.getSimpleName()) ) {
-                    evals.add(classMap.get(stdClass.getSimpleName()));
-                }
-            }
-        }
-
-        // Get the specific classes provided.
-        for ( String module : modulesToUse ) {
-            if ( !classMap.containsKey(module) ) {
-                throw new UserException.CommandLineException("Module " + module + " could not be found; please check that you have specified the class name correctly");
-            }
-
-            if ( classMap.containsKey(module) ) {
-                evals.add(classMap.get(module));
-            }
-        }
-
-        return evals;
-    }
-
-    /**
-     * Recursively initialize the evaluation contexts
-     *
-     * @param stratificationObjects  the stratifications to use
-     * @param evaluationObjects      the evaluations to use
-     * @param stratStack             a stack of stratifications to apply
-     * @param ec                     evaluation context
-     * @return  a map of all the evaluation contexts
-     */
-    private HashMap<StateKey, NewEvaluationContext> initializeEvaluationContexts(Set<VariantStratifier> stratificationObjects,  Set<Class<? extends VariantEvaluator>> evaluationObjects, Stack<VariantStratifier> stratStack, NewEvaluationContext ec) {
-        HashMap<StateKey, NewEvaluationContext> ecs = new HashMap<StateKey, NewEvaluationContext>();
-
-        if (stratStack == null) {
-            stratStack = new Stack<VariantStratifier>();
-            stratStack.addAll(stratificationObjects);
-        }
-
-        if (!stratStack.isEmpty()) {
-            Stack<VariantStratifier> newStratStack = new Stack<VariantStratifier>();
-            newStratStack.addAll(stratStack);
-
-            VariantStratifier vs = newStratStack.pop();
-
-            for ( String state : vs.getAllStates() ) {
-                NewEvaluationContext nec = new NewEvaluationContext();
-                if (ec != null) {
-                    nec.putAll(ec);
-                }
-                nec.put(vs, state);
-
-                ecs.putAll(initializeEvaluationContexts(stratificationObjects, evaluationObjects, newStratStack, nec));
-            }
-        } else {
-            HashMap<StateKey, NewEvaluationContext> necs = new HashMap<StateKey, NewEvaluationContext>();
-
-            StateKey stateKey = new StateKey();
-            for ( VariantStratifier vs : ec.keySet() ) {
-                String state = ec.get(vs);
-
-                stateKey.put(vs.getClass().getSimpleName(), state);
-            }
-
-            ec.addEvaluationClassList(this, stateKey, evaluationObjects);
-
-            necs.put(stateKey, ec);
-
-            return necs;
-        }
-
-        return ecs;
-    }
-
-    /**
-     * Initialize the output report
-     *
-     * @param stratificationObjects  the stratifications to use
-     * @param evaluationObjects      the evaluations to use
-     * @return  an initialized report object
-     */
-    private GATKReport initializeGATKReport(Set<VariantStratifier> stratificationObjects, Set<Class<? extends VariantEvaluator>> evaluationObjects) {
-        GATKReport report = new GATKReport();
-
-        for ( Class<? extends VariantEvaluator> ve : evaluationObjects ) {
-            String tableName = ve.getSimpleName();
-            String tableDesc = ve.getAnnotation(Analysis.class).description();
-
-            report.addTable(tableName, tableDesc);
-
-            GATKReportTable table = report.getTable(tableName);
-            table.addPrimaryKey("entry", false);
-            table.addColumn(tableName, tableName);
-
-            for ( VariantStratifier vs : stratificationObjects ) {
-                String columnName = vs.getClass().getSimpleName();
-
-                table.addColumn(columnName, "unknown");
-            }
-
-            try {
-                VariantEvaluator vei = ve.newInstance();
-                vei.initialize(this);
-
-                AnalysisModuleScanner scanner = new AnalysisModuleScanner(vei);
-                Map<Field, DataPoint> datamap = scanner.getData();
-
-                for (Field field : datamap.keySet()) {
-                    field.setAccessible(true);
-
-                    if (! (field.get(vei) instanceof TableType) ) {
-                        table.addColumn(field.getName(), 0.0);
-                    }
-                }
-            } catch (InstantiationException e) {
-                throw new StingException("InstantiationException: " + e);
-            } catch (IllegalAccessException e) {
-                throw new StingException("IllegalAccessException: " + e);
-            }
-        }
-
-        return report;
-    }
+    // Utility class
+    private final VariantEvalUtils variantEvalUtils = new VariantEvalUtils(this);
 
     /**
      * Initialize the stratifications, evaluations, evaluation contexts, and reporting object
      */
     public void initialize() {
         // Just list the modules, and exit quickly.
-        if (LIST) { listModulesAndExit(); }
+        if (LIST) { variantEvalUtils.listModulesAndExit(); }
 
         // Categorize each rod as an eval or a comp rod.
         for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
@@ -386,7 +156,11 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
         sampleNamesForStratification.add(ALL_SAMPLE_NAME);
 
         // Initialize select expressions
-        jexlExpressions.addAll(VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS));
+        //jexlExpressions.addAll(VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS));
+        for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
+            SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
+            jexlExpressions.add(sjexl);
+        }
 
         // Add select expressions for anything in the tranches file
         if ( TRANCHE_FILENAME != null ) {
@@ -399,253 +173,14 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
         }
 
         // Initialize the set of stratifications and evaluations to use
-        stratificationObjects = initializeStratificationObjects(NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
-        Set<Class<? extends VariantEvaluator>> evaluationObjects = initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
+        stratificationObjects = variantEvalUtils.initializeStratificationObjects(NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
+        Set<Class<? extends VariantEvaluator>> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
 
         // Initialize the evaluation contexts
-        evaluationContexts = initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);
+        evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);
 
         // Initialize report table
-        report = initializeGATKReport(stratificationObjects, evaluationObjects);
-    }
-
-    /**
-     * Figure out what the allowable variation types are based on the eval context
-     *
-     * @param tracker    the reference metadata tracker
-     * @param ref        the reference context
-     * @param compNames  the comp track names
-     * @param evalNames  the evaluation track names
-     * @return  the set of allowable variation types
-     */
-    private EnumSet<VariantContext.Type> getAllowableVariationTypes(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> compNames, Set<String> evalNames) {
-        EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.NO_VARIATION);
-
-        if (tracker != null) {
-            Collection<VariantContext> evalvcs = tracker.getVariantContexts(ref, evalNames, null, ref.getLocus(), true, false);
-
-            for ( VariantContext vc : evalvcs ) {
-                allowableTypes.add(vc.getType());
-            }
-
-            if (allowableTypes.size() == 1) {
-                // We didn't find any variation in the eval track, so now let's look at the comp track for allowable types
-                Collection<VariantContext> compvcs = tracker.getVariantContexts(ref, compNames, null, ref.getLocus(), true, false);
-
-                for ( VariantContext vc : compvcs ) {
-                    allowableTypes.add(vc.getType());
-                }
-            }
-        }
-
-        return allowableTypes;
-    }
-
-    /**
-     * Subset a VariantContext to a single sample
-     *
-     * @param vc  the VariantContext object containing multiple samples
-     * @param sampleName  the sample to pull out of the VariantContext
-     * @return  a new VariantContext with just the requested sample
-     */
-    private VariantContext getSubsetOfVariantContext(VariantContext vc, String sampleName) {
-        ArrayList<String> sampleNames = new ArrayList<String>();
-        sampleNames.add(sampleName);
-
-        return getSubsetOfVariantContext(vc, sampleNames);
-    }
-
-    /**
-     * Subset a VariantContext to a set of samples
-     *
-     * @param vc  the VariantContext object containing multiple samples
-     * @param sampleNames  the samples to pull out of the VariantContext
-     * @return  a new VariantContext with just the requested samples
-     */
-    private VariantContext getSubsetOfVariantContext(VariantContext vc, Collection<String> sampleNames) {
-        VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values());
-
-        HashMap<String,Object> newAts = new HashMap<String,Object>(vcsub.getAttributes());
-
-        int originalAlleleCount = vc.getHetCount() + 2*vc.getHomVarCount();
-        int newAlleleCount = vcsub.getHetCount() + 2*vcsub.getHomVarCount();
-
-        if (originalAlleleCount == newAlleleCount && newAlleleCount == 1) {
-            newAts.put("ISSINGLETON", true);
-        }
-
-        VariantContextUtils.calculateChromosomeCounts(vcsub, newAts, true);
-        vcsub = VariantContext.modifyAttributes(vcsub,newAts);
-
-        logger.debug(String.format("VC %s subset to %s AC%n", vc.getSource(), vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)));
-
-        return vcsub;
-    }
-
-    /**
-     * For a list of track names, bind the variant contexts to a trackName->sampleName->VariantContext mapping.
-     * Additional variant contexts per sample are automatically generated and added to the map unless the
-     * sample name matches the ALL_SAMPLE_NAME constant.
-     *
-     * @param tracker         the metadata tracker
-     * @param ref             the reference context
-     * @param trackNames      the list of track names to process
-     * @param allowableTypes  a set of allowable variation types
-     * @param byFilter        if false, only accept PASSing VariantContexts.  Otherwise, accept both PASSing and filtered sites
-     * @param trackPerSample  if false, don't stratify per sample (and don't cut up the VariantContext like we would need to do this)
-     * @param allowNoCalls    if false, don't accept no-call loci from a variant track
-     * @return  a mapping of track names to a list of VariantContext objects
-     */
-    private HashMap<String, HashMap<String, VariantContext>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> trackNames, EnumSet<VariantContext.Type> allowableTypes, boolean byFilter, boolean trackPerSample, boolean allowNoCalls) {
-        HashMap<String, HashMap<String, VariantContext>> bindings = new HashMap<String, HashMap<String, VariantContext>>();
-
-        for ( String trackName : trackNames ) {
-            HashMap<String, VariantContext> vcs = new HashMap<String, VariantContext>();
-
-            Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(ref, trackName, allowableTypes, ref.getLocus(), true, true);
-            VariantContext vc = contexts != null && contexts.size() == 1 ? contexts.iterator().next() : null;
-
-            // First, filter the VariantContext to represent only the samples for evaluation
-            if ( vc != null ) {
-                VariantContext vcsub = vc;
-
-                if (vc.hasGenotypes() && vc.hasGenotypes(sampleNamesForEvaluation)) {
-                    vcsub = getSubsetOfVariantContext(vc, sampleNamesForEvaluation);
-                }
-
-                if ((byFilter || !vcsub.isFiltered()) && (allowNoCalls || vcsub.getType() != VariantContext.Type.NO_VARIATION)) {
-                    vcs.put(ALL_SAMPLE_NAME, vcsub);
-                }
-
-                // Now, if stratifying, split the subsetted vc per sample and add each as a new context
-                if ( vc.hasGenotypes() && trackPerSample ) {
-                    for ( String sampleName : sampleNamesForEvaluation ) {
-                        VariantContext samplevc = getSubsetOfVariantContext(vc, sampleName);
-    
-                        if ((byFilter || !samplevc.isFiltered()) && (allowNoCalls || samplevc.getType() != VariantContext.Type.NO_VARIATION)) {
-                            vcs.put(sampleName, samplevc);
-                        }
-                    }
-                }
-
-                bindings.put(trackName, vcs);
-            }
-        }
-
-        return bindings;
-    }
-
-    /**
-     * Maps track names to sample name to VariantContext objects.  For eval tracks, VariantContexts per specified
-     * sample are also included.
-     *
-     * @param tracker      the metadata tracker
-     * @param ref          the reference context
-     * @param compNames    the list of comp names to process
-     * @param evalNames    the list of eval names to process
-     * @return  a mapping of track names to a list of VariantContext objects
-     */
-    private HashMap<String, HashMap<String, VariantContext>> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set<String> compNames, Set<String> evalNames) {
-        HashMap<String, HashMap<String, VariantContext>> vcs = new HashMap<String, HashMap<String, VariantContext>>();
-
-        EnumSet<VariantContext.Type> allowableTypes = getAllowableVariationTypes(tracker, ref, compNames, evalNames);
-
-        boolean byFilter = false;
-        boolean perSampleIsEnabled = false;
-        for (VariantStratifier vs : stratificationObjects) {
-            if (vs.getClass().getSimpleName().equals("Filter")) {
-                byFilter = true;
-            } else if (vs.getClass().getSimpleName().equals("Sample")) {
-                perSampleIsEnabled = true;
-            }
-        }
-
-        HashMap<String, HashMap<String, VariantContext>> evalBindings = bindVariantContexts(tracker, ref, evalNames, allowableTypes, byFilter, perSampleIsEnabled, true);
-        HashMap<String, HashMap<String, VariantContext>> compBindings = bindVariantContexts(tracker, ref, compNames, allowableTypes, byFilter, false, false);
-
-        vcs.putAll(compBindings);
-        vcs.putAll(evalBindings);
-
-        return vcs;
-    }
-
-    /**
-     * Recursively initialize the state keys used to look up the right evaluation context based on the state of the variant context
-     *
-     * @param stateMap    the map of allowable states
-     * @param stateStack  a stack of the states
-     * @param stateKey    a state key object
-     * @param stateKeys   all the state keys
-     * @return  a list of state keys
-     */
-    private ArrayList<StateKey> initializeStateKeys(HashMap<VariantStratifier, ArrayList<String>> stateMap, Stack<HashMap<VariantStratifier, ArrayList<String>>> stateStack, StateKey stateKey, ArrayList<StateKey> stateKeys) {
-        if (stateStack == null) {
-            stateStack = new Stack<HashMap<VariantStratifier, ArrayList<String>>>();
-
-            for ( VariantStratifier vs : stateMap.keySet() ) {
-                HashMap<VariantStratifier, ArrayList<String>> oneSetOfStates = new HashMap<VariantStratifier, ArrayList<String>>();
-                oneSetOfStates.put(vs, stateMap.get(vs));
-
-                stateStack.add(oneSetOfStates);
-            }
-        }
-
-        if (!stateStack.isEmpty()) {
-            Stack<HashMap<VariantStratifier, ArrayList<String>>> newStateStack = new Stack<HashMap<VariantStratifier, ArrayList<String>>>();
-            newStateStack.addAll(stateStack);
-
-            HashMap<VariantStratifier, ArrayList<String>> oneSetOfStates = newStateStack.pop();
-            VariantStratifier vs = oneSetOfStates.keySet().iterator().next();
-
-            for ( String state : oneSetOfStates.get(vs)) {
-                StateKey newStateKey = new StateKey();
-                if (stateKey != null) {
-                    newStateKey.putAll(stateKey);
-                }
-
-                newStateKey.put(vs.getClass().getSimpleName(), state);
-
-                initializeStateKeys(stateMap, newStateStack, newStateKey, stateKeys);
-            }
-        } else {
-            stateKeys.add(stateKey);
-
-            return stateKeys;
-        }
-
-        return stateKeys;
-    }
-
-    /**
-     * Return the number of samples being used
-     * @return the number of samples
-     */
-    public int getNumSamples() {
-        return numSamples;
-    }
-
-    /**
-     * Return the minimum phasing quality to be used with the GenotypePhasingEvaluator module
-     * @return  the minimum phasing quality
-     */
-    public double getMinPhaseQuality() {
-        return MIN_PHASE_QUALITY;
-    }
-
-    /**
-     * Return the family structure to be used with the MendelianViolationEvaluator module
-     * @return  the family structure string
-     */
-    public String getFamilyStructure() {
-        return FAMILY_STRUCTURE;
-    }
-
-    /**
-     * Return the mendelian violation qual threshold to be used with the MendelianViolationEvaluator module
-     * @return   the mendelian violation qual threshold
-     */
-    public double getMendelianViolationQualThreshold() {
-        return MENDELIAN_VIOLATION_QUAL_THRESHOLD;
+        report = variantEvalUtils.initializeGATKReport(stratificationObjects, evaluationObjects);
     }
 
     /**
@@ -659,32 +194,34 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
             }
         }
 
-        //      track           sample  vc
-        HashMap<String, HashMap<String, VariantContext>> vcs = getVariantContexts(tracker, ref, compNames, evalNames);
+        if (tracker != null) {
+            //      track           sample  vc
+            HashMap<String, HashMap<String, VariantContext>> vcs = variantEvalUtils.getVariantContexts(tracker, ref, compNames, evalNames);
 
-        for ( String compName : compNames ) {
-            VariantContext comp = vcs.containsKey(compName) && vcs.get(compName) != null && vcs.get(compName).containsKey(ALL_SAMPLE_NAME) ? vcs.get(compName).get(ALL_SAMPLE_NAME) : null;
+            for ( String compName : compNames ) {
+                VariantContext comp = vcs.containsKey(compName) && vcs.get(compName) != null && vcs.get(compName).containsKey(ALL_SAMPLE_NAME) ? vcs.get(compName).get(ALL_SAMPLE_NAME) : null;
 
-            for ( String evalName : evalNames ) {
-                for ( String sampleName : sampleNamesForStratification ) {
-                    VariantContext eval = vcs.containsKey(evalName) && vcs.get(evalName) != null ? vcs.get(evalName).get(sampleName) : null;
+                for ( String evalName : evalNames ) {
+                    for ( String sampleName : sampleNamesForStratification ) {
+                        VariantContext eval = vcs.containsKey(evalName) && vcs.get(evalName) != null ? vcs.get(evalName).get(sampleName) : null;
 
-                    HashMap<VariantStratifier, ArrayList<String>> stateMap = new HashMap<VariantStratifier, ArrayList<String>>();
-                    for ( VariantStratifier vs : stratificationObjects ) {
-                        ArrayList<String> states = vs.getRelevantStates(ref, comp, compName, eval, evalName, sampleName);
-                        stateMap.put(vs, states);
-                    }
+                        HashMap<VariantStratifier, ArrayList<String>> stateMap = new HashMap<VariantStratifier, ArrayList<String>>();
+                        for ( VariantStratifier vs : stratificationObjects ) {
+                            ArrayList<String> states = vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName);
+                            stateMap.put(vs, states);
+                        }
 
-                    ArrayList<StateKey> stateKeys = new ArrayList<StateKey>();
-                    initializeStateKeys(stateMap, null, null, stateKeys);
+                        ArrayList<StateKey> stateKeys = new ArrayList<StateKey>();
+                        variantEvalUtils.initializeStateKeys(stateMap, null, null, stateKeys);
 
-                    HashSet<StateKey> stateKeysHash = new HashSet<StateKey>(stateKeys);
+                        HashSet<StateKey> stateKeysHash = new HashSet<StateKey>(stateKeys);
 
-                    for ( StateKey stateKey : stateKeysHash ) {
-                        NewEvaluationContext nec = evaluationContexts.get(stateKey);
+                        for ( StateKey stateKey : stateKeysHash ) {
+                            NewEvaluationContext nec = evaluationContexts.get(stateKey);
 
-                        synchronized (nec) {
-                            nec.apply(tracker, ref, context, comp, eval);
+                            synchronized (nec) {
+                                nec.apply(tracker, ref, context, comp, eval);
+                            }
                         }
                     }
                 }
@@ -694,38 +231,13 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
         return null;
     }
 
-    /**
-     * A composite, 'reduce of reduces' function.
-     *
-     * @param lhs 'left-most' portion of data in the composite reduce.
-     * @param rhs 'right-most' portion of data in the composite reduce.
-     * @return The composite reduce type.
-     */
-    public Integer treeReduce(Integer lhs, Integer rhs) {
-        return null;
-    }
+    public Integer treeReduce(Integer lhs, Integer rhs) { return null; }
 
-    /**
-     * Provide an initial value for reduce computations.
-     *
-     * @return Initial value of reduce.
-     */
     @Override
-    public Integer reduceInit() {
-        return null;
-    }
+    public Integer reduceInit() { return null; }
 
-    /**
-     * Reduces a single map with the accumulator provided as the ReduceType.
-     *
-     * @param value result of the map.
-     * @param sum   accumulator for the reduce.
-     * @return accumulator with result of the map taken into account.
-     */
     @Override
-    public Integer reduce(Integer value, Integer sum) {
-        return null;
-    }
+    public Integer reduce(Integer value, Integer sum) { return null; }
 
     /**
      * Output the finalized report
@@ -822,4 +334,31 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
 
         report.print(out);
     }
+
+    // Accessors
+    public Logger getLogger() { return logger; }
+
+    public int getNumSamples() { return numSamples; }
+
+    public double getMinPhaseQuality() { return MIN_PHASE_QUALITY; }
+
+    public String getFamilyStructure() { return FAMILY_STRUCTURE; }
+
+    public double getMendelianViolationQualThreshold() { return MENDELIAN_VIOLATION_QUAL_THRESHOLD; }
+
+    public TreeSet<VariantStratifier> getStratificationObjects() { return stratificationObjects; }
+
+    public static String getAllSampleName() { return ALL_SAMPLE_NAME; }
+
+    public Set<String> getKnownNames() { return knownNames; }
+
+    public Set<String> getEvalNames() { return evalNames; }
+
+    public Set<String> getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
+
+    public Set<String> getSampleNamesForStratification() { return sampleNamesForStratification; }
+
+    public Set<String> getCompNames() { return compNames; }
+
+    public Set<SortableJexlVCMatchExp> getJexlExpressions() { return jexlExpressions; }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index 97e721a4b..e02154bb9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -19,18 +19,17 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
  */
 @Analysis(description = "The overlap between eval and comp sites")
 public class CompOverlap extends VariantEvaluator implements StandardEval {
-
     @DataPoint(description = "number of eval SNP sites")
-    long nEvalSNPs = 0;
+    long nEvalVariants = 0;
 
     @DataPoint(description = "number of comp SNP sites")
-    long nCompSNPs = 0;
+    long nCompVariants = 0;
 
     @DataPoint(description = "number of eval sites outside of comp sites")
     long novelSites = 0;
 
     @DataPoint(description = "number of eval sites at comp sites")
-    long nSNPsAtComp = 0;
+    long nVariantsAtComp = 0;
 
     @DataPoint(description = "percentage of eval sites at comp sites")
     double compRate = 0.0;
@@ -45,9 +44,9 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
         return 2;   // we need to see each eval track and each comp track
     }
 
-    public long nNovelSites() { return nEvalSNPs - nSNPsAtComp; }
-    public double compRate() { return rate(nSNPsAtComp, nEvalSNPs); }
-    public double concordanceRate() { return rate(nConcordant, nSNPsAtComp); }
+    public long nNovelSites() { return nEvalVariants - nVariantsAtComp; }
+    public double compRate() { return rate(nVariantsAtComp, nEvalVariants); }
+    public double concordanceRate() { return rate(nConcordant, nVariantsAtComp); }
 
     public void finalizeEvaluation() {
         compRate = 100 * compRate();
@@ -76,21 +75,18 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
     }
 
     public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        //boolean expectingIndels = false;
+        boolean evalIsGood = eval != null;
+        boolean expectingIndels = eval != null && eval.isIndel();
 
-        //boolean compIsGood = expectingIndels ? comp != null && comp.isNotFiltered() && comp.isIndel() : comp != null && comp.isNotFiltered() && comp.isSNP() ;
-        //boolean evalIsGood = expectingIndels ? eval != null && eval.isIndel() : eval != null && eval.isSNP() ;
+        boolean compIsGood = expectingIndels ? comp != null && comp.isNotFiltered() && comp.isIndel() : comp != null && comp.isNotFiltered() && comp.isSNP() ;
 
-        boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP() ;
-        boolean evalIsGood = eval != null && eval.isSNP() ;
-
-        if (compIsGood) nCompSNPs++;           // count the number of comp events
-        if (evalIsGood) nEvalSNPs++;           // count the number of eval events
+        if (compIsGood) nCompVariants++;           // count the number of comp events
+        if (evalIsGood) nEvalVariants++;           // count the number of eval events
 
         if (compIsGood && evalIsGood) {
-            nSNPsAtComp++;
+            nVariantsAtComp++;
 
-            if (!discordantP(eval, comp)) {     // count whether we're concordant or not with the comp value
+            if (!discordantP(eval, comp)) {    // count whether we're concordant or not with the comp value
                 nConcordant++;
             }
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 26fa3baab..0fdef754f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -1,18 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
+import org.apache.log4j.Logger;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFConstants;
-import org.broadinstitute.sting.gatk.contexts.*;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
-import org.broadinstitute.sting.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.report.utils.TableType;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
index a2b548404..9fbcea5bc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index 285695526..5364e7b87 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -4,9 +4,9 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.report.utils.TableType;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
index 82c95a4ba..e61540c32 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
@@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.report.utils.TableType;
 
 import java.util.ArrayList;
@@ -157,8 +157,7 @@ public class IndelMetricsByAC extends VariantEvaluator {
         }
 
         public String toString() {
-            String returnString = "";
-            return returnString;
+            return "";
         }
 
         public void incrValue( VariantContext eval ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
index 03fa2f7c6..97a5669a7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
@@ -474,10 +474,6 @@ public class IndelStatistics extends VariantEvaluator {
         return getName();
     }
 
-    //public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
-        //return null;
-    //}
-
     public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
 
         if (eval != null ) {
@@ -502,13 +498,9 @@ public class IndelStatistics extends VariantEvaluator {
 
         return null; // This module doesn't capture any interesting sites, so return null
     }
-    public String update0(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
 
-        return null;
-    }
     public void finalizeEvaluation() {
-    //
-       int k=0; 
+        int k=0;
     }
 
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index bf162d88d..6d73310c4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -3,18 +3,18 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
 import java.util.Arrays;
-import java.util.regex.Pattern;
+import java.util.List;
 import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Mendelian violation detection and counting
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
index b7e965ead..457ca4d4d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
@@ -11,8 +11,8 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
-import org.broadinstitute.sting.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.report.utils.TableType;
 
 import java.util.ArrayList;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
index f79211d62..735ca70eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
@@ -31,9 +31,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.report.utils.TableType;
 
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
index cf3b70432..22483f224 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
@@ -3,6 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -13,7 +15,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         this.compNames = compNames;
 
         states = new ArrayList<String>();
@@ -24,7 +26,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add(compName);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
index 20f3de1ad..9af9fd518 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
@@ -3,6 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -11,7 +13,7 @@ public class CpG extends VariantStratifier implements StandardStratification {
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         states = new ArrayList<String>();
         states.add("all");
         states.add("CpG");
@@ -22,7 +24,7 @@ public class CpG extends VariantStratifier implements StandardStratification {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         boolean isCpG = false;
         if (ref != null && ref.getBases() != null) {
             String fwRefBases = new String(ref.getBases());
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
index dbe2262dc..eccc737ff 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
@@ -3,6 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -14,7 +16,7 @@ public class Degeneracy extends VariantStratifier {
     private HashMap<String, String> degeneracies;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         states = new ArrayList<String>();
         states.add("1-fold");
         states.add("2-fold");
@@ -52,7 +54,7 @@ public class Degeneracy extends VariantStratifier {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("all");
@@ -61,10 +63,9 @@ public class Degeneracy extends VariantStratifier {
             String type = null;
             String aa = null;
 
-            if (eval.getAttributeAsString("refseq.functionalClass") != null) {
-                type = eval.getAttributeAsString("refseq.functionalClass");
+            if (eval.hasAttribute("refseq.functionalClass")) {
                 aa = eval.getAttributeAsString("refseq.variantAA");
-            } else if (eval.getAttributeAsString("refseq.functionalClass_1") != null) {
+            } else if (eval.hasAttribute("refseq.functionalClass_1")) {
                 int annotationId = 1;
                 String key;
 
@@ -85,7 +86,7 @@ public class Degeneracy extends VariantStratifier {
                     }
 
                     annotationId++;
-                } while (eval.getAttributeAsString(key) != null);
+                } while (eval.hasAttribute(key));
             }
 
             if (aa != null && degeneracies.containsKey(aa)) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
index 1f475bb28..faf0ab245 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
@@ -3,6 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -13,7 +15,7 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         this.evalNames = evalNames;
 
         states = new ArrayList<String>();
@@ -24,7 +26,7 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add(evalName);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
index 35c97c704..316300396 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
@@ -3,6 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -12,7 +14,7 @@ public class Filter extends VariantStratifier {
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         states = new ArrayList<String>();
         states.add("called");
         states.add("filtered");
@@ -23,7 +25,7 @@ public class Filter extends VariantStratifier {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("raw");
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
index 4db03e1ee..609e604a6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
@@ -3,6 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -12,7 +14,7 @@ public class FunctionalClass extends VariantStratifier {
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         states = new ArrayList<String>();
         states.add("all");
         states.add("silent");
@@ -24,7 +26,7 @@ public class FunctionalClass extends VariantStratifier {
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
 
         relevantStates.add("all");
@@ -32,9 +34,9 @@ public class FunctionalClass extends VariantStratifier {
         if (eval != null && eval.isVariant()) {
             String type = null;
 
-            if (eval.getAttributeAsString("refseq.functionalClass") != null) {
+            if (eval.hasAttribute("refseq.functionalClass")) {
                 type = eval.getAttributeAsString("refseq.functionalClass");
-            } else if (eval.getAttributeAsString("refseq.functionalClass_1") != null) {
+            } else if (eval.hasAttribute("refseq.functionalClass_1")) {
                 int annotationId = 1;
                 String key;
 
@@ -43,7 +45,7 @@ public class FunctionalClass extends VariantStratifier {
 
                     String newtype = eval.getAttributeAsString(key);
 
-                    if ( newtype != null &&
+                    if ( newtype != null && !newtype.equalsIgnoreCase("null") &&
                          ( type == null ||
                          ( type.equals("silent") && !newtype.equals("silent") ) ||
                          ( type.equals("missense") && newtype.equals("nonsense") ) )
@@ -52,7 +54,7 @@ public class FunctionalClass extends VariantStratifier {
                     }
 
                     annotationId++;
-                } while (eval.getAttributeAsString(key) != null);
+                } while (eval.hasAttribute(key));
             }
 
             if (type != null) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
index 4e94ef03e..ce980e3f5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
@@ -3,22 +3,24 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
 
 public class JexlExpression extends VariantStratifier implements StandardStratification {
     // needs to know the jexl expressions
-    private Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions;
+    private Set<SortableJexlVCMatchExp> jexlExpressions;
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         this.jexlExpressions = jexlExpressions;
 
         states = new ArrayList<String>();
         states.add("none");
-        for ( VariantContextUtils.JexlVCMatchExp jexlExpression : jexlExpressions ) {
+        for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) {
             states.add(jexlExpression.name);
         }
     }
@@ -27,11 +29,11 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
         relevantStates.add("none");
 
-        for ( VariantContextUtils.JexlVCMatchExp jexlExpression : jexlExpressions ) {
+        for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) {
             if (eval != null && VariantContextUtils.match(eval, jexlExpression)) {
                 relevantStates.add(jexlExpression.name);
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
index a4a1822ce..e55bd496e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
@@ -3,8 +3,12 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.EnumSet;
 import java.util.Set;
 
 public class Novelty extends VariantStratifier implements StandardStratification {
@@ -13,7 +17,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
     private ArrayList<String> states;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         this.knownNames = knownNames;
 
         states = new ArrayList<String>();
@@ -26,11 +30,29 @@ public class Novelty extends VariantStratifier implements StandardStratification
         return states;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
-        ArrayList<String> relevantStates = new ArrayList<String>();
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+        boolean isNovel = true;
 
+        if (tracker != null) {
+            for (String knownName : knownNames) {
+                if (tracker.hasROD(knownName)) {
+                    EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.NO_VARIATION);
+                    if (eval != null) {
+                        allowableTypes.add(eval.getType());
+                    }
+
+                    Collection<VariantContext> knownComps = tracker.getVariantContexts(ref, knownName, allowableTypes, ref.getLocus(), true, true);
+
+                    isNovel = knownComps.size() == 0;
+
+                    break;
+                }
+            }
+        }
+
+        ArrayList<String> relevantStates = new ArrayList<String>();
         relevantStates.add("all");
-        relevantStates.add(comp == null ? "novel" : "known");
+        relevantStates.add(isNovel ? "novel" : "known");
 
         return relevantStates;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
index 4c73031d8..d95ede0b2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
@@ -3,7 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -13,7 +14,7 @@ public class Sample extends VariantStratifier {
     private ArrayList<String> samples;
 
     @Override
-    public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
         samples = new ArrayList<String>();
         samples.addAll(sampleNames);
     }
@@ -22,7 +23,7 @@ public class Sample extends VariantStratifier {
         return samples;
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         ArrayList<String> relevantStates = new ArrayList<String>();
         relevantStates.add(sampleName);
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
index 5717958de..8bfdcc3d1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
@@ -4,18 +4,19 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 
 import java.util.ArrayList;
 import java.util.Set;
 
 public abstract class VariantStratifier implements Comparable {
-    public abstract void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames);
+    public abstract void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames);
 
     public ArrayList<String> getAllStates() {
         return new ArrayList<String>();
     }
 
-    public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         return null;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
index 4faa9c42f..44248e169 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
@@ -52,40 +52,35 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
 
     public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) {
         for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
-            //synchronized ( this ) {
-                // we always call update0 in case the evaluation tracks things like number of bases covered
-                //evaluation.update0(tracker, ref, context);
+            // we always call update0 in case the evaluation tracks things like number of bases covered
 
-                // the other updateN methods don't see a null context
-                if ( tracker == null )
-                    continue;
+            // the other updateN methods don't see a null context
+            if ( tracker == null )
+                continue;
 
-                // now call the single or paired update function
-                switch ( evaluation.getComparisonOrder() ) {
-                    case 1:
-                        if (eval != null) {
-                            evaluation.update1(eval, tracker, ref, context);
-                        }
+            // now call the single or paired update function
+            switch ( evaluation.getComparisonOrder() ) {
+                case 1:
+                    if (eval != null) {
+                        evaluation.update1(eval, tracker, ref, context);
+                    }
 
-                        break;
-                    case 2:
-                        //if (eval != null) {
-                            evaluation.update2(eval, comp, tracker, ref, context);
-                        //}
+                    break;
+                case 2:
+                    //if (eval != null) {
+                        evaluation.update2(eval, comp, tracker, ref, context);
+                    //}
 
-                        break;
-                    default:
-                        throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
-                }
-            //}
+                    break;
+                default:
+                    throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
+            }
         }
     }
 
     public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        //synchronized (this) {
-            for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
-                evaluation.update0(tracker, ref, context);
-            }
-        //}
+        for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
+            evaluation.update0(tracker, ref, context);
+        }
     }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 9ae1b58d3..fc57e97c0 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -9,6 +9,9 @@ import java.util.HashMap;
 import java.util.Map;
 
 public class VariantEvalIntegrationTest extends WalkerTest {
+    private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval";
+    private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
+
     private static String cmdRoot = "-T VariantEval" +
             " -R " + b36KGReference;
 
@@ -18,18 +21,301 @@ public class VariantEvalIntegrationTest extends WalkerTest {
             " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
 
     private static String rootGZ = cmdRoot +
-                " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
-                " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
-                " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
+            " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
+            " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
+            " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
 
     private static String[] testsEnumerations = {root, rootGZ};
 
+    private String cmdLineBuilder(String ... arguments) {
+        String cmdline = "";
+
+        for ( int argIndex = 0; argIndex < arguments.length; argIndex++ ) {
+            cmdline += arguments[argIndex];
+
+            if (argIndex < arguments.length - 1) {
+                cmdline += " ";
+            }
+        }
+
+        return cmdline;
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndels() {
+//        nProcessedLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38
+//        nCalledLoci    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -c PASS = 9
+//        nRefLoci       = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 == ".") print $0 }' | wc -l = 4
+//        nVariantLoci   = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != ".") print $0 }' | wc -l = 5
+//        variantRate    = nVariantLoci / nProcessedLoci = 0.131578947
+//        nSNPs          = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != "." && length($4) == 1 && length($5) == 1) print $0 }' | wc -l = 3
+//        nInsertions    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != "." && length($5) > 1) print $0 }' | wc -l = 1
+//        nDeletions     = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($5 != "." && length($4) > 1) print $0 }' | wc -l = 1
+//        nNoCalls       = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "[[:punct:]]/[[:punct:]]") print $0 }' | wc -l = 4
+//        nHets          = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/1" || $i ~ "1/0") print $0 }' | wc -l = 8
+//        nHomRef        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/0") print $0 }' | wc -l = 10
+//        nHomVar        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                                cmdLineBuilder(
+                                        "-T VariantEval",
+                                        "-R " + b37KGReference,
+                                        "-D " + b37dbSNP129,
+                                        "-B:eval,VCF " + fundamentalTestVCF,
+                                        "-noEV",
+                                        "-EV CountVariants",
+                                        "-noST",
+                                        "-BTI eval",
+                                        "-o %s"
+                                ),
+                                1,
+                                Arrays.asList("476b495de54e1a377c6895c02a6fdf6a")
+                              );
+        executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() {
+//        nProcessedLociKnown = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38
+//        nCalledLociKnown    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }'= 3
+//        nVariantLociKnown   = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | wc -l = 3
+//        variantRateKnown    = nVariantLoci / nProcessedLoci = 0.0789473684
+//        nSNPsKnown          = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != "." && length($5) == 1) print $0 }' | wc -l = 3
+//        nInsertionsKnown    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != "." && length($5) > 1) print $0 }' | wc -l = 0
+//        nDeletionsKnown     = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != "." && length($4) > 1) print $0 }' | wc -l = 0
+//        nNoCallsKnown       = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "[[:punct:]]/[[:punct:]]") print $0 }' | wc -l = 0
+//        nHetsKnown          = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/1" || $i ~ "1/0") print $0 }' | wc -l = 3
+//        nHomRefKnown        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/0") print $0 }' | wc -l = 1
+//        nHomVarKnown        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST Novelty",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("9f4e4fff339e725f42d65063e43e7d1c")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() {
+//        nProcessedLociFail  = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38
+//        nCalledLociFail     = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -vc PASS = 3
+//        nRefLociFail        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ if ($5 == ".") print $0 }' | wc -l = 1
+//        nVariantLociFail    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ if ($5 != ".") print $0 }' | wc -l = 2
+//        nSNPsFail           = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ if ($5 != "." && length($4) == 1 && length($5) == 1) print $0 }' | wc -l = 1
+//        nInsertionsFail     = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ if ($5 != "." && length($5) > 1) print $0 }' | wc -l = 0
+//        nDeletionsFail      = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ if ($5 != "." && length($4) > 1) print $0 }' | wc -l = 1
+//        nNoCallsFail        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "[[:punct:]]/[[:punct:]]") print $0 }' | wc -l = 3
+//        nHetsFail           = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/1" || $i ~ "1/0") print $0 }' | wc -l = 1
+//        nHomRefFail         = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/0") print $0 }' | wc -l = 2
+//        nHomVarFail         = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 3
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST Novelty",
+                        "-ST Filter",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("369fa4f37bcc03b8a0bc1e58bf22bf0a")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithCpG() {
+//        nProcessedLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38
+//        nCalledLoci    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep -c PASS = 8
+//        nRefLoci       = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ if ($5 == ".") print $0 }' | wc -l = 3
+//        nVariantLoci   = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ if ($5 != ".") print $0 }' | wc -l = 5
+//        nSNPs          = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ if ($5 != "." && length($4) == 1 && length($5) == 1) print $0 }' | wc -l = 3
+//        nInsertions    = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ if ($5 != "." && length($5) > 1) print $0 }' | wc -l = 1
+//        nDeletions     = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ if ($5 != "." && length($4) > 1) print $0 }' | wc -l = 1
+//        nNoCalls       = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "[[:punct:]]/[[:punct:]]") print $0 }' | wc -l = 4
+//        nHets          = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/1" || $i ~ "1/0") print $0 }' | wc -l = 8
+//        nHomRef        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "0/0") print $0 }' | wc -l = 10
+//        nHomVar        = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST CpG",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("891ad0d38f1a1b08b31fe1cb6a3afc04")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST FunctionalClass",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("d588179e2d9ed6e92a6ae1a80ac04270")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST Degeneracy",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("ceb0f5d9e0ea99eb8d00bce2f7bc1b73")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithSample() {
+//        HG00513
+//          nSNPs = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if (length($4) == 1 && length($5) == 1) print $0 }' | awk '{ print $10 }' | grep -v '0/0' | grep -v '\.\/\.' | wc -l = 3
+//          nInsertions = $ grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if (length($4) == 1 && length($5) > 1) print $0 }' | awk '{ print $10 }' | grep -v '0/0' | grep -v '\.\/\.' | wc -l = 1
+//          nDeletions = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if (length($4) > 1 && length($5) == 1) print $0 }' | awk '{ print $10 }' | grep -v '0/0' | grep -v '\.\/\.' | wc -l = 0
+//          nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($10 ~ "[[:punct:]]/[[:punct:]]") print $0 }' | wc -l = 2
+//          nHets = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($10 ~ "0/1") print $0 }' | wc -l = 2
+//          nHomRef = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($10 ~ "0/0") print $0 }' | wc -l = 3
+//          nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($10 ~ "1/1") print $0 }' | wc -l = 2
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST Sample",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("94ce29b34b9e2e4304fc1bbf3f971a7d")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression() {
+//        nSNPs = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $0 }' | wc -l = 7
+//        nRefLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20 && $6 == ".") print $0 }' | wc -l = 4
+//        nVariantLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20 && $6 != ".") print $0 }' | wc -l = 3
+//        nSNPs = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20 && length($5) == 1 && length($6) == 1 && $6 != ".") print $0 }' | wc -l = 3
+//        nHomRef = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '0/0' = 9
+//        nHets = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '0/1' = 3
+//        nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '1/1' = 5
+//        nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '\.\/\.' = 4
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST JexlExpression",
+                        "-select 'DP < 20'",
+                        "-selectName DepthSelect",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("96de32970b204816ecd9a120b9d8782b")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
+    }
+
+    @Test
+    public void testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions() {
+//        nSNPs = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $0 }' | wc -l = 7
+//        nRefLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20 && $6 == ".") print $0 }' | wc -l = 4
+//        nVariantLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20 && $6 != ".") print $0 }' | wc -l = 3
+//        nSNPs = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20 && length($5) == 1 && length($6) == 1 && $6 != ".") print $0 }' | wc -l = 3
+//        nHomRef = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '0/0' = 9
+//        nHets = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '0/1' = 3
+//        nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '1/1' = 5
+//        nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '\.\/\.' = 4
+        WalkerTestSpec spec = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-D " + b37dbSNP129,
+                        "-B:eval,VCF " + fundamentalTestVCF,
+                        "-noEV",
+                        "-EV CountVariants",
+                        "-noST",
+                        "-ST JexlExpression",
+                        "-select 'DP < 20'",
+                        "-selectName DepthLt20",
+                        "-select 'DP > 20'",
+                        "-selectName DepthGt20",
+                        "-BTI eval",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("aea882132eb6afdc93fbc70e8d6c50e2")
+        );
+        executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
+    }
+
     @Test
     public void testSelect1() {
         String extraArgs = "-L 1:1-10,000,000";
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
-                    1, Arrays.asList("c803c90f587796146286217ab30930a3"));
+                    1, Arrays.asList("4184a8d44f8c559c904e41edf464a467"));
             executeTestParallel("testSelect1", spec);
             //executeTest("testSelect1", spec);
         }
@@ -50,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         for (String vcfFile : vcfFiles) {
             WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
                     1,
-                    Arrays.asList("bb16335f9510bcab2bd14a4299afd879"));
+                    Arrays.asList("1387fcf8d5c53ff2c820fe79cc999bcf"));
             executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
             //executeTest("testVEGenotypeConcordance" + vcfFile, spec);
         }
@@ -60,8 +346,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        expectations.put("-L 1:1-10,000,000", "47990cfb955720421c29991954af4450");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "ce7bb86e6281b1aef1ad94f9ba7301a9");
+        expectations.put("-L 1:1-10,000,000", "b28516b4d3627d2eb017a5449284a4e4");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "a49d897095586ddb72bfe9faf0291312");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -84,10 +370,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
 
 
-        String matchingMD5 = "6388fbad81b0f281298812496fd3ed6c";
-        expectations.put("", matchingMD5);
-        expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5);
-        expectations.put(" -knownName comp_hapmap", "6388fbad81b0f281298812496fd3ed6c");
+        expectations.put("", "65d74eb7eea2355989c389e8fa886c06");
+        expectations.put(" -knownName comp_hapmap -knownName dbsnp", "776827cd5a6fcaf8b8508813e8dc023c");
+        expectations.put(" -knownName comp_hapmap", "e99a89cbca2027c983edc00d31ea4ec9");
         for (String tests : testsEnumerations) {
             for (Map.Entry<String, String> entry : expectations.entrySet()) {
                 String extraArgs2 = entry.getKey();
@@ -102,6 +387,79 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         }
     }
 
+    @Test
+    public void testCompVsEvalAC() {
+        String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("49cb4a6126c5383abd9a49a6c22b8d93"));
+        executeTestParallel("testCompVsEvalAC",spec);
+        //executeTest("testCompVsEvalAC",spec);
+    }
+
+    private static String withSelect(String cmd, String select, String name) {
+        return String.format("%s -select '%s' -selectName %s", cmd, select, name);
+    }
+
+    @Test
+    public void testTranches() {
+        String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
+        executeTestParallel("testTranches",spec);
+        //executeTest("testTranches",spec);
+    }
+
+    @Test
+    public void testCompOverlap() {
+        String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e8b5561eb60ea98a9be4a45abee00e07"));
+        executeTestParallel("testCompOverlap",spec);
+        //executeTest("testCompOverlap",spec);
+    }
+
+    @Test
+    public void testEvalTrackWithoutGenotypes() {
+        String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
+
+        String extraArgs = "-T VariantEval -R " +
+                           b37KGReference +
+                           " -L 20" +
+                           " -D " + dbsnp +
+                           " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+                           " -noST -ST Novelty -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9323a6ad62dedbdb08752411960db60f"));
+        executeTestParallel("testEvalTrackWithoutGenotypes",spec);
+    }
+
+    @Test
+    public void testMultipleEvalTracksWithoutGenotypes() {
+        String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
+
+        String extraArgs = "-T VariantEval -R " + b37KGReference +
+                " -L 20" +
+                " -D " + dbsnp +
+                " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+                " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
+                " -noST -ST Novelty -o %s";
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ef23195331affd332af1de9d261fdd0a"));
+        executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
+    }
+
+    @Test
+    public void testMultipleCompTracks() {
+        String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf";
+
+        String extraArgs =  "-T VariantEval" +
+                           " -R " + b37KGReference +
+                           " -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
+                           " -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
+                           " -B:dbsnp,VCF " + dbsnp +
+                           " -L 20:10000000-10100000" +
+                           " -noST -noEV -ST Novelty -EV CompOverlap" +
+                           " -o %s";
+
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("3fced8e5fa7a1c952d08fead0accd3fb"));
+        executeTestParallel("testMultipleCompTracks",spec);
+    }
+
 //    @Test
 //    public void testVEGenomicallyAnnotated() {
 //        String vecmd = "-T VariantEval" +
@@ -129,81 +487,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 //            //executeTest("testVEWriteVCF", spec);
 //        }
 //    }
-
-    @Test
-    public void testCompVsEvalAC() {
-        String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d8d59ec86ec9e00abad4ec44741de22f"));
-        executeTestParallel("testCompVsEvalAC",spec);
-        //executeTest("testCompVsEvalAC",spec);
-    }
-
-    private static String withSelect(String cmd, String select, String name) {
-        return String.format("%s -select '%s' -selectName %s", cmd, select, name);
-    }
-
-    @Test
-    public void testTranches() {
-        String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
-        executeTestParallel("testTranches",spec);
-        //executeTest("testTranches",spec);
-    }
-
-    @Test
-    public void testCompOverlap() {
-        String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81377be26bf8fa32339d01c173428f7d"));
-        executeTestParallel("testCompOverlap",spec);
-        //executeTest("testCompOverlap",spec);
-    }
-
-    @Test
-    public void testEvalTrackWithoutGenotypes() {
-        String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
-
-        String extraArgs = "-T VariantEval -R " +
-                           b37KGReference +
-                           " -L 20" +
-                           " -D " + dbsnp +
-                           " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
-                           " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2e2c24b49f699506b967befbde5a6fa8"));
-        executeTestParallel("testEvalTrackWithoutGenotypes",spec);
-    }
-
-    @Test
-    public void testMultipleEvalTracksWithoutGenotypes() {
-        String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
-
-        String extraArgs = "-T VariantEval -R " + b37KGReference +
-                " -L 20" +
-                " -D " + dbsnp +
-                " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
-                " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
-                " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("144053b8bef5a79b23d0abd17b561294"));
-        executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
-    }
-
-    @Test
-    public void testMultipleCompTracks() {
-        String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf";
-
-        String extraArgs =  "-T VariantEval" +
-                           " -R " + b37KGReference +
-                           " -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
-                           " -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
-                           " -B:dbsnp,VCF " + dbsnp +
-                           " -L 20:10000000-10100000" +
-                           " -noST -noEV -ST Novelty -EV CompOverlap" +
-                           " -o %s";
-
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2d2c6e7850ec964624bb032d24834e2f"));
-        executeTestParallel("testMultipleCompTracks",spec);
-    }
-
-
+//
 //    @Test
 //    public void testVEValidatePass() {
 //        String extraArgs = "-L 1:1-10,000,000";
@@ -227,4 +511,5 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 //    private static String withValidateTiTv(String cmd, double min, double max) {
 //        return String.format("%s -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio >= %2$s' -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio <= %3$s'", cmd, min, max);
 //    }
+
 }