VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E).

Generalized some of the packaging code from VariantAnnotator.  Matt might want to take a look to make this nicer...?



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3925 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -63,7 +63,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     protected String[] annotationsToUse = {};
 
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
-    protected String[] annotationClassesToUse = { };
+    protected String[] annotationGroupsToUse = {};
 
     @Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
     protected Boolean USE_ALL_ANNOTATIONS = false;
@@ -131,7 +131,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         if ( USE_ALL_ANNOTATIONS )
             engine = new VariantAnnotatorEngine(getToolkit());
         else
-            engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
+            engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse);
 
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -60,8 +60,8 @@ public class VariantAnnotatorEngine {
 
     public static final String dbPrefix = "comp";
 
-    private ArrayList<InfoFieldAnnotation> requestedInfoAnnotations;
+    private List<InfoFieldAnnotation> requestedInfoAnnotations;
-    private ArrayList<GenotypeAnnotation> requestedGenotypeAnnotations;
+    private List<GenotypeAnnotation> requestedGenotypeAnnotations;
 
     private HashMap<String, String> dbAnnotations = new HashMap<String, String>();
 
@@ -82,16 +82,14 @@ public class VariantAnnotatorEngine {
 
     // use this constructor if you want all possible annotations
     public VariantAnnotatorEngine(GenomeAnalysisEngine engine) {
-        List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class);
+        requestedInfoAnnotations = PackageUtils.getInstancesOfClassesImplementingInterface(InfoFieldAnnotation.class);
-        requestedInfoAnnotations = getInstances(infoAnnotationClasses);
+        requestedGenotypeAnnotations = PackageUtils.getInstancesOfClassesImplementingInterface(GenotypeAnnotation.class);
-        List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = PackageUtils.getClassesImplementingInterface(GenotypeAnnotation.class);
-        requestedGenotypeAnnotations = getInstances(genotypeAnnotationClasses);
-
         initialize(engine);
     }
 
     // use this constructor if you want to select specific annotations (and/or interfaces)
-    public VariantAnnotatorEngine(GenomeAnalysisEngine engine, String[] annotationClassesToUse, String[] annotationsToUse) {
+    public VariantAnnotatorEngine(GenomeAnalysisEngine engine, String[] annotationGroupsToUse, String[] annotationsToUse) {
+
         // create a map for all annotation classes which implement our top-level interfaces
         HashMap<String, Class> classMap = new HashMap<String, Class>();
         for ( Class c : PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class) )
@@ -103,7 +101,7 @@ public class VariantAnnotatorEngine {
 
         HashSet<Class> classes = new HashSet<Class>();
         // get the classes from the provided groups (interfaces)
-        for ( String group : annotationClassesToUse ) {
+        for ( String group : annotationGroupsToUse ) {
             Class interfaceClass = classMap.get(group);
             if ( interfaceClass == null )
                 interfaceClass = classMap.get(group + "Annotation");
@@ -128,31 +126,14 @@ public class VariantAnnotatorEngine {
         for ( Class c : classes ) {
             // note that technically an annotation can work on both the INFO and FORMAT fields
             if ( InfoFieldAnnotation.class.isAssignableFrom(c) )
-                requestedInfoAnnotations.add((InfoFieldAnnotation)getInstance(c));
+                requestedInfoAnnotations.add((InfoFieldAnnotation)PackageUtils.getSimpleInstance(c));
             if ( GenotypeAnnotation.class.isAssignableFrom(c) )
-                requestedGenotypeAnnotations.add((GenotypeAnnotation)getInstance(c));
+                requestedGenotypeAnnotations.add((GenotypeAnnotation)PackageUtils.getSimpleInstance(c));
         }
 
         initialize(engine);
     }
 
-    private static <T> ArrayList<T> getInstances(List<Class<? extends T>> classes) {
-        ArrayList<T> objects = new ArrayList<T>();
-        for ( Class c : classes )
-            objects.add((T)getInstance(c));
-        return objects;
-    }
-
-    private static <T> T getInstance(Class<T> c) {
-        try {
-            return c.newInstance();
-        } catch (InstantiationException e) {
-            throw new StingException(String.format("Cannot instantiate annotation class '%s': must be concrete class", c.getSimpleName()));
-        } catch (IllegalAccessException e) {
-            throw new StingException(String.format("Cannot instantiate annotation class '%s': must have no-arg constructor", c.getSimpleName()));
-        }
-    }
-
     private void initialize(GenomeAnalysisEngine engine) {
 
         // check to see whether comp rods were included
@@ -181,15 +162,8 @@ public class VariantAnnotatorEngine {
         return descriptions;
     }
 
-    /**
+    // A slightly simplified interface for when you don't have any reads, so the stratifiedContexts aren't necessary, and
-     * A slightly simplified interface for when you don't have any reads, so the stratifiedContexts aren't necessary, and
+    // you only permit a single return value
-     * you only permit a single return value
-     *
-     * @param tracker
-     * @param ref
-     * @param vc
-     * @return
-     */
     public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc) {
         Collection<VariantContext> results = this.annotateContext(tracker, ref, EMPTY_STRATIFIED_ALIGNMENT_CONTEXT, vc);
 
@@ -278,13 +252,7 @@ public class VariantAnnotatorEngine {
         return returnValue;
     }
 
-    /**
+    // Finish processing data from GenomicAnnotation.
-     * Finish processing data from GenomicAnnotation.
-     *
-     * @param infoAnnotationOutputsList
-     * @param annotationsForCurrentLocusFromAllAnnotatorInputTables
-     * @return
-     */
     private List<Map<String, Object>> processGenomicAnnotation( List<Map<String, Object>> infoAnnotationOutputsList, Map<String, Object> annotationsForCurrentLocusFromAllAnnotatorInputTables)
     {
 
@@ -330,15 +298,8 @@ public class VariantAnnotatorEngine {
         return infoAnnotationOutputsList;
     }
 
-    /**
+   // Performs a join between the an info field record represented by outputRecordInfoField and the infoAnnotationOutputsList.
-     * Performs a join between the an info field record represented by outputRecordInfoField and the infoAnnotationOutputsList.
+   private List<Map<String, Object>> performJoin( List<Map<String, Object>> infoAnnotationOutputsList,  Map<String, Object> outputRecordInfoField, JoinTable joinTable)
-     *
-     * @param infoAnnotationOutputsList
-     * @param outputRecordInfoField
-     * @param joinTable
-     * @return
-     */
-    private List<Map<String, Object>> performJoin( List<Map<String, Object>> infoAnnotationOutputsList,  Map<String, Object> outputRecordInfoField, JoinTable joinTable)
     {
         //System.err.println("Looking at: " + joinTable.getLocalBindingName()+ "- join to " + joinTable.getExternalBindingName() + "." + joinTable.getExternalColumnName() );
         //for the current joinTable, for each output line, find the externalJoinColumnValue and see if it matches the joinColumnValue of any record(s) in this joinTable.
@@ -413,16 +374,10 @@ public class VariantAnnotatorEngine {
     }
 
 
-    /**
+    // Implements not-oneToMany mode, where the output lines have a one-to-one relationship
-     * Implements not-oneToMany mode, where the output lines have a one-to-one relationship
+    // with the input variants, and all multiple-match records are collapsed into the single info field.
-     * with the input variants, and all multiple-match records are collapsed into the single info field.
+    // The collapsing is done by appending an _i to each key name (where 'i' is a record counter), as well
-     * The collapsing is done by appending an _i to each key name (where 'i' is a record counter), as well
+    // as a special bindingName.numMatchingRecords=n key-value pair which specifies the upper limit of the counter.
-     * as a special bindingName.numMatchingRecords=n key-value pair which specifies the upper limit of the counter.
-     *
-     * @param infoAnnotationOutputsList
-     * @param matchingRecords
-     * @param bindingName
-     */
     private void addToExistingAnnotationOutputs(
             final List<Map<String, Object>> infoAnnotationOutputsList,
             final List<Map<String, String>> matchingRecords,
@@ -470,19 +425,12 @@ public class VariantAnnotatorEngine {
         }
     }
 
-    /**
+    // Implements oneToMany mode. Takes the current infoAnnotationOutputsList
-     * Implements oneToMany mode. Takes the current infoAnnotationOutputsList
+    // (where each element represents a line in the output VCF file), and
-     * (where each element represents a line in the output VCF file), and
+    // generates a new infoAnnotationOutputsList which contains one copy of the current
-     * generates a new infoAnnotationOutputsList which contains one copy of the current
+    // infoAnnotationOutputs for each record matchingRecords.
-     * infoAnnotationOutputs for each record matchingRecords.
+    // The returned list will have size:
-     * The returned list will have size:
+    // infoAnnotationOutputsList.size() * matchingRecords.size()
-     * infoAnnotationOutputsList.size() * matchingRecords.size()
-     *
-     * @param infoAnnotationOutputsList
-     * @param matchingRecords
-     * @param bindingName
-     * @return
-     */
     private List<Map<String, Object>> explodeInfoAnnotationOutputsList(
             final List<Map<String, Object>> infoAnnotationOutputsList,
             final List<Map<String, String>> matchingRecords,
@@ -515,8 +463,8 @@ public class VariantAnnotatorEngine {
      * Records statistics for the explodeInfoAnnotationOutputsList(..) calculation.
      * @param bindingName The table from which annotations were gotten
      * @param numNewVCFRecordsAnnotatedWithBindingNameData The number of new output VCF records created with annotations from this table
-     * @param infoAnnotationOutputsList
+     * @param infoAnnotationOutputsList output list
-     * @parma matchingRecordsSize
+     * @param matchingRecordsSize  matching records size
      */
     private void recordStats( final String bindingName, int numNewVCFRecordsAnnotatedWithBindingNameData, final List<Map<String, Object>> infoAnnotationOutputsList, int matchingRecordsSize ) {
 
@@ -549,13 +497,7 @@ public class VariantAnnotatorEngine {
     }
 
 
-
+    // Applies the -S arg to the results
-    /**
-     * Applies the -S arg to the results
-     *
-     * @param infoAnnotationOutputsList
-     * @return The new newInfoAnnotationOutputList with -S arg applied.
-     */
     private List<Map<String, Object>> applySelectArg( final List<Map<String, Object>> infoAnnotationOutputsList )
     {
         final List<Map<String, Object>> newInfoAnnotationOutputList = new LinkedList<Map<String, Object>>();
@@ -614,7 +556,7 @@ public class VariantAnnotatorEngine {
      *
      * See class-level comments for more details.
      *
-     * @param oneToMany
+     * @param oneToMany true if we should break out from one to many
      */
     public void setOneToMany(boolean oneToMany) {
         this.oneToMany = oneToMany;
@@ -694,9 +636,7 @@ public class VariantAnnotatorEngine {
     }
 
 
-    /**
+    //Returns a map containing stats on how many output vcf records were annotated from each database
-     * Returns a map containing stats on how many output vcf records were annotated from each database
-     */
     public Map<String, Integer> getInputTableHitCounter() {
         return Collections.unmodifiableMap(inputTableHitCounter);
     }

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CompOverlap.java

@@ -18,7 +18,7 @@ import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
 @Analysis(name = "Comp Overlap", description = "the overlap between eval and comp sites")
-public class CompOverlap extends VariantEvaluator {
+public class CompOverlap extends VariantEvaluator implements StandardEval {
 
     @DataPoint(name = "eval sites", description = "number of eval SNP sites")
     long nEvalSNPs = 0;

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java

@@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.StingException;
 
 
 @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
-public class CountVariants extends VariantEvaluator {
+public class CountVariants extends VariantEvaluator implements StandardEval {
 
     // the following fields are in output order:
 

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java

@@ -37,7 +37,7 @@ import java.util.*;
  */
 
 @Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
-public class GenotypeConcordance extends VariantEvaluator {
+public class GenotypeConcordance extends VariantEvaluator implements StandardEval {
     private static final boolean PRINT_INTERESTING_SITES = true;
 
     protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java

@@ -8,7 +8,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.StingException;
-import org.broad.tribble.vcf.VCFGenotypeRecord;
 
 import java.util.ArrayList;
 
@@ -43,7 +42,7 @@ import java.util.ArrayList;
  */
 
 @Analysis(name = "Quality Metrics by allele count", description = "Shows various stats binned by allele count")
-public class SimpleMetricsByAC extends VariantEvaluator {
+public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval {
     // a mapping from quality score histogram bin to Ti/Tv ratio
     @DataPoint(name="TiTv by AC", description = "TiTv by allele count")
     MetricsByAc metrics = null;

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/StandardEval.java

@@ -0,0 +1,28 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.varianteval;
+
+public interface StandardEval {}

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java

@@ -8,7 +8,7 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 
 @Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator")
-public class TiTvVariantEvaluator extends VariantEvaluator {
+public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
 
     @DataPoint(name = "ti_count", description = "number of transition loci")
     long nTi = 0;

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -136,11 +136,11 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     //
     // Arguments for choosing which modules to run
     //
-    @Argument(fullName="evalModule", shortName="E", doc="One or more specific eval modules to apply to the eval track(s)", required=false)
+    @Argument(fullName="evalModule", shortName="E", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noStandard is specified)", required=false)
     protected String[] modulesToUse = {};
 
-    @Argument(fullName="useNoModules", shortName="none", doc="Use no eval modules", required=false)
+    @Argument(fullName="doNotUseAllStandardModules", shortName="noStandard", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)")
-    protected Boolean USE_NO_MODULES = false;
+    protected Boolean NO_STANDARD = false;
 
     @Argument(fullName="list", shortName="ls", doc="List the available eval modules and exit")
     protected Boolean LIST = false;
@@ -272,7 +272,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     }
 
     // Dynamically determined variantEvaluation classes
-    private List<Class<? extends VariantEvaluator>> evaluationClasses = null;
+    private Set<Class<? extends VariantEvaluator>> evaluationClasses = null;
 
     /** output writer for interesting sites */
     private VCFWriter writer = null;
@@ -392,21 +392,23 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         for ( Class<? extends VariantEvaluator> c : PackageUtils.getClassesImplementingInterface(VariantEvaluator.class) )
             classMap.put(c.getSimpleName(), c);
 
-        if ( USE_NO_MODULES ) {
+        evaluationClasses = new HashSet<Class<? extends VariantEvaluator>>();
-            evaluationClasses = new ArrayList<Class<? extends VariantEvaluator>>(0);
+
-        } else if ( modulesToUse.length == 0 ) {
+        // by default, use standard eval modules
-            evaluationClasses = new ArrayList<Class<? extends VariantEvaluator>>(classMap.values());
+        if ( !NO_STANDARD ) {
-        } else {
+            for ( Class<? extends StandardEval> myClass : PackageUtils.getClassesImplementingInterface(StandardEval.class) ) {
-            // get the specific classes provided
+                if ( classMap.containsKey(myClass.getSimpleName()) )
-            evaluationClasses = new ArrayList<Class<? extends VariantEvaluator>>(modulesToUse.length);
+                    evaluationClasses.add(classMap.get(myClass.getSimpleName()));
-            for ( String module : modulesToUse ) {
-                Class<? extends VariantEvaluator> moduleClass = classMap.get(module);
-                if ( moduleClass == null )
-                    throw new StingException("Class " + module + " is not found; please check that you have specified the class name correctly");
-                evaluationClasses.add(moduleClass);
             }
         }
 
+        // get the specific classes provided
+        for ( String module : modulesToUse ) {
+            if ( !classMap.containsKey(module) )
+                throw new StingException("Class " + module + " is not found; please check that you have specified the class name correctly");
+            evaluationClasses.add(classMap.get(module));
+        }
+
         for ( VariantEvaluator e : instantiateEvalationsSet() ) {
             // for collecting purposes
             variantEvaluationNames.add(e.getName());

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -28,10 +28,9 @@ package org.broadinstitute.sting.utils.classloader;
 import org.reflections.Reflections;
 import org.reflections.scanners.ResourcesScanner;
 import org.reflections.scanners.SubTypesScanner;
-import org.reflections.util.ClasspathHelper;
 import org.reflections.util.ConfigurationBuilder;
 import org.reflections.util.ManifestAwareClasspathHelper;
-import org.slf4j.LoggerFactory;
+import org.broadinstitute.sting.utils.StingException;
 
 import java.net.URL;
 import java.util.Set;
@@ -81,6 +80,24 @@ public class PackageUtils {
         return concreteTypes;
     }
 
+    public static <T> List<T> getInstancesOfClassesImplementingInterface(Class<T> iface) {
+        List<Class<? extends T>> classes = PackageUtils.getClassesImplementingInterface(iface);
+        List<T> instances = new ArrayList<T>();
+        for ( Class<? extends T> c : classes )
+            instances.add(getSimpleInstance(c));
+        return instances;
+    }
+
+    public static <T> T getSimpleInstance(Class<T> c) {
+        try {
+            return c.newInstance();
+        } catch (InstantiationException e) {
+            throw new StingException(String.format("Cannot instantiate class '%s': must be concrete class", c.getSimpleName()));
+        } catch (IllegalAccessException e) {
+            throw new StingException(String.format("Cannot instantiate class '%s': must have no-arg constructor", c.getSimpleName()));
+        }
+    }
+
     /**
      * Return the interface classes that extend the specified interface.
      *

java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -29,7 +29,7 @@ public class
         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("119601d7e9e67a1053663b2e546250ed"));
+                    1, Arrays.asList("a12bd969ca3bc676752e078d205c730a"));
             executeTest("testSelect1", spec);
         }
     }
@@ -38,7 +38,7 @@ public class
     public void testSelect2() {
         String extraArgs = "-L 1:1-10,000,000";
         WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
-                1, Arrays.asList("06d495ab8169a2570eebdc54ecdffe10"));
+                1, Arrays.asList("2c1a99b225b55dcf605410ba5e6be789"));
         executeTest("testSelect2", spec);
     }
 
@@ -46,7 +46,7 @@ public class
     public void testVEGenotypeConcordance() {
         String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
         for (String vcfFile : vcfFiles) {
-            WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
+            WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -noStandard -E GenotypeConcordance -reportType CSV -o %s",
                     1,
                     Arrays.asList("15d1075d384da2bb7445f7493f2b6a07"));
             executeTest("testVEGenotypeConcordance" + vcfFile, spec);
@@ -57,8 +57,8 @@ public class
     @Test
     public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        expectations.put("-L 1:1-10,000,000", "629b8b124306435ff56b66357354dfbc");
+        expectations.put("-L 1:1-10,000,000", "a48e4ca3a019bf46eb3a178a6a80822f");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "f51c299d500b347d098c7ab25f54a436");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0 -E MendelianViolationEvaluator", "bc35dfefce72899d4c673bfc37c9a7f3");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -75,15 +75,15 @@ public class
     @Test
     public void testVEComplex() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30" +
+        String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator" +
                 " -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
                 " -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
 
 
-        String matchingMD5 = "d01725ce4e46c8fea0855a923c1598fd";
+        String matchingMD5 = "38c8906cc364d04ba39a437d93d752d3";
         expectations.put("", matchingMD5);
         expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
-        expectations.put(" -known comp_hapmap", "a50be9240f6c90503fb6333d8a78b974");
+        expectations.put(" -known comp_hapmap", "b839c8e9f26b01281899f86362b5323c");
         for (String tests : testsEnumerations) {
             for (Map.Entry<String, String> entry : expectations.entrySet()) {
                 String extraArgs2 = entry.getKey();
@@ -103,7 +103,7 @@ public class
                        "-R " + oneKGLocation + "reference/human_b36_both.fasta " +
                        "-L 21 " +
                        "-D " + GATKDataLocation + "dbsnp_129_b36.rod " +
-                       "-E CountFunctionalClasses " +
+                       "-E CountFunctionalClasses -noStandard " +
                        "-B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf " +
                        "-o %s";
         String md5 = "d41d8cd98f00b204e9800998ecf8427e";
@@ -114,11 +114,11 @@ public class
 
     @Test
     public void testVEWriteVCF() {
-        String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
+        String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator";
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
                     2,
-                    Arrays.asList("483f821ce96f4cf571e9bba356c9f325", "989bc30dea6c8a4cf771cd1b9fdab488"));
+                    Arrays.asList("8059c6b53ba15598bf89d65c79742566", "989bc30dea6c8a4cf771cd1b9fdab488"));
             executeTest("testVEWriteVCF", spec);
         }
     }