- New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs.

- VariantAnnotatorEngine changed to call genotype annotations even if pilups and allele -> likelihood mappings are not present. Current genotype annotations altered to check for null pilupes and null mappings.

public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java

@@ -29,6 +29,7 @@ import com.google.common.base.Function;
 import com.google.common.collect.Collections2;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.help.GATKDocUtils;
 
 import java.util.Collection;
 import java.util.List;
@@ -68,16 +69,29 @@ public class FilterManager extends PluginManager<ReadFilter> {
     @Override
     protected String formatErrorMessage(String pluginCategory, String pluginName) {
         List<Class<? extends ReadFilter>> availableFilters = this.getPluginsImplementing(ReadFilter.class);
-        Collection<String> availableFilterNames = Collections2.transform(availableFilters, new Function<Class<? extends ReadFilter>,String>(){
 
-            @Override
-            public String apply(final Class<? extends ReadFilter> input) {
-                return getName(input);
-            }
-        });
 
-        return String.format("Read filter %s not found. Available read filters:%n%s.%n%n%s",pluginName,
-                Utils.join(String.format(", "),availableFilterNames),
+        return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
+                userFriendlyListofReadFilters(availableFilters),
                 "Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
     }
+
+    private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {
+        final String headName = "FilterName", headDoc = "Documentation";
+        int longestNameLength = -1;
+        for ( Class < ? extends ReadFilter> filter : filters ) {
+            longestNameLength = Math.max(longestNameLength,this.getName(filter).length());
+        }
+        String format = "   %"+longestNameLength+"s        %s%n";
+
+        StringBuilder listBuilder = new StringBuilder();
+        listBuilder.append(String.format(format,headName,headDoc));
+        for ( Class<? extends ReadFilter> filter : filters ) {
+            String helpLink = GATKDocUtils.helpLinksToGATKDocs(filter);
+            String filterName = this.getName(filter);
+            listBuilder.append(String.format(format,filterName,helpLink));
+        }
+
+        return listBuilder.toString();
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java

@@ -33,6 +33,9 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim
                          final Genotype g,
                          final GenotypeBuilder gb,
                          final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
+        if ( stratifiedContext == null )
+            return;
+
         Double ratio = annotateSNP(stratifiedContext, vc, g);
         if (ratio == null)
             return;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java

@@ -54,7 +54,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
                          final Genotype g,
                          final GenotypeBuilder gb,
                          final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
-        if ( g == null || !g.isCalled() )
+        if ( g == null || !g.isCalled() || ( stratifiedContext == null && alleleLikelihoodMap == null) )
             return;
 
         if (alleleLikelihoodMap != null && !alleleLikelihoodMap.isEmpty())

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java

@@ -55,7 +55,7 @@ public class MappingQualityZeroBySample extends GenotypeAnnotation {
                          final Genotype g,
                          final GenotypeBuilder gb,
                          final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
-        if ( g == null || !g.isCalled() )
+        if ( g == null || !g.isCalled() || stratifiedContext == null )
             return;
 
         int mq0 = 0;

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

@@ -300,16 +300,12 @@ public class VariantAnnotatorEngine {
             if (stratifiedPerReadAlleleLikelihoodMap != null)
                 perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());
 
-            if ( context == null && perReadAlleleLikelihoodMap == null) {
-                // no likelihoods nor pileup available: just move on to next sample
-                genotypes.add(genotype);
-            } else {
-                final GenotypeBuilder gb = new GenotypeBuilder(genotype);
-                for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
-                    annotation.annotate(tracker, walker, ref, context, vc, genotype, gb, perReadAlleleLikelihoodMap);
-                }
-                genotypes.add(gb.make());
+
+            final GenotypeBuilder gb = new GenotypeBuilder(genotype);
+            for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
+                annotation.annotate(tracker, walker, ref, context, vc, genotype, gb, perReadAlleleLikelihoodMap);
             }
+            genotypes.add(gb.make());
         }
 
         return genotypes;

public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java

@@ -27,6 +27,8 @@ package org.broadinstitute.sting.utils.classloader;
 
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
+import org.broadinstitute.sting.gatk.WalkerManager;
+import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -276,8 +278,16 @@ public class PluginManager<PluginType> {
      */
     public PluginType createByName(String pluginName) {
         Class<? extends PluginType> plugin = pluginsByName.get(pluginName);
-        if( plugin == null )
-            throw new UserException(formatErrorMessage(pluginCategory,pluginName));
+        if( plugin == null ) {
+            String errorMessage = formatErrorMessage(pluginCategory,pluginName);
+            if ( this.getClass().isAssignableFrom(FilterManager.class) ) {
+                throw new UserException.MalformedReadFilterException(errorMessage);
+            } else if ( this.getClass().isAssignableFrom(WalkerManager.class) ) {
+                throw new UserException.MalformedWalkerArgumentsException(errorMessage);
+            } else {
+                throw new UserException.CommandLineException(errorMessage);
+            }
+        }
         try {
             return plugin.newInstance();
         } catch (Exception e) {

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -63,6 +63,18 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class MalformedReadFilterException extends CommandLineException {
+        public MalformedReadFilterException(String message) {
+            super(String.format("Malformed read filter: %s",message));
+        }
+    }
+
+    public static class MalformedWalkerArgumentsException extends CommandLineException {
+        public MalformedWalkerArgumentsException(String message) {
+            super(String.format("Malformed walker argument: %s",message));
+        }
+    }
+
     public static class MalformedGenomeLoc extends UserException {
         public MalformedGenomeLoc(String message, GenomeLoc loc) {
             super(String.format("Badly formed genome loc: %s: %s", message, loc));

public/java/test/org/broadinstitute/sting/commandline/InvalidArgumentIntegrationTest.java

@@ -0,0 +1,41 @@
+package org.broadinstitute.sting.commandline;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+import org.testng.annotations.Test;
+import org.testng.annotations.DataProvider;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 8/31/12
+ * Time: 11:03 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class InvalidArgumentIntegrationTest extends WalkerTest {
+    private static final String callsB36  = BaseTest.validationDataLocation + "lowpass.N3.chr1.raw.vcf";
+
+    private WalkerTest.WalkerTestSpec baseTest(String flag, String arg, Class exeption) {
+        return new WalkerTest.WalkerTestSpec("-T VariantsToTable -M 10 --variant:vcf "
+                + callsB36 + " -F POS,CHROM -R "
+                + b36KGReference +  " -o %s " + flag + " " + arg,
+                1, exeption);
+
+    }
+
+    @Test
+    public void testUnknownReadFilter() {
+        executeTest("UnknownReadFilter",baseTest("-rf","TestUnknownReadFilter", UserException.MalformedReadFilterException.class));
+    }
+
+    @Test
+    public void testMalformedWalkerArgs() {
+        executeTest("MalformedWalkerArgs",
+                new WalkerTest.WalkerTestSpec("-T UnknownWalkerName -M 10 --variant:vcf "
+                + callsB36 + " -F POS,CHROM -R "
+                + b36KGReference +  " -o %s ",
+                1, UserException.MalformedWalkerArgumentsException.class));
+    }
+}