Continuing progress towards RodBinding 1.0

-- Cleaning up old interface to RMDT, docs and contracts added
-- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type

public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java

@@ -292,21 +292,33 @@ public class RefMetaDataTracker {
     }
 
     /**
-     * Helper function for getFirst() operations that takes a list of <T> and
+     * Get all of the RMD tracks at the current site. Each track is returned as a single compound
-     * returns the first element, or null if no such element exists.
+     * object (RODRecordList) that may contain multiple RMD records associated with the current site.
      *
-     * @param l
+     * @return List of all tracks
-     * @param <T>
-     * @return
      */
-    @Requires({"l != null"})
+    public List<RODRecordList> getBoundRodTracks() {
-    final private <T extends Feature> T safeGetFirst(final List<T> l) {
+        return new ArrayList<RODRecordList>(map.values());
-        return l.isEmpty() ? null : l.get(0);
     }
 
+    /**
+     * The number of tracks with at least one value bound here
+     * @return the number of tracks with at least one bound Feature
+     */
+    public int getNTracksWithBoundFeatures() {
+        return map.size();
+    }
+
+    // ------------------------------------------------------------------------------------------
     //
-    // Deprecated accessors -- will be removed
     //
+    // old style accessors
+    //
+    // TODO -- DELETE ME
+    //
+    //
+    // ------------------------------------------------------------------------------------------
+
     @Deprecated
     public boolean hasValues(final String name) {
         return map.containsKey(canonicalName(name));
@@ -333,73 +345,27 @@ public class RefMetaDataTracker {
         return safeGetFirst(getValues(type, name, onlyAtThisLoc));
     }
 
-    /**
+    // ------------------------------------------------------------------------------------------
-     * Get all of the RMDs at the current site. The collection is "flattened": for any track that has multiple records
+    //
-     * at the current site, they all will be added to the list as separate elements.
+    //
-     *
+    // Private utility functions
-     * @return collection of all rods
+    //
-     */
+    //
-    @Deprecated
+    // ------------------------------------------------------------------------------------------
-    public List<GATKFeature> getAllValuesAsGATKFeatures() {
-        List<GATKFeature> l = new ArrayList<GATKFeature>();
-        for ( RODRecordList rl : map.values() ) {
-            if ( rl != null )
-                l.addAll(rl);
-        }
-        return l;
-    }
 
     /**
-     * Get all of the RMD tracks at the current site. Each track is returned as a single compound
+     * Helper function for getFirst() operations that takes a list of <T> and
-     * object (RODRecordList) that may contain multiple RMD records associated with the current site.
+     * returns the first element, or null if no such element exists.
      *
-     * @return List of all tracks
+     * @param l
-     */
+     * @param <T>
-    public List<RODRecordList> getBoundRodTracks() {
-        return new ArrayList<RODRecordList>(map.values());
-    }
-
-    /**
-     * The number of tracks with at least one value bound here
      * @return
      */
-    public int getNumberOfTracksWithValue() {
+    @Requires({"l != null"})
-        int n = 0;
+    final private <T extends Feature> T safeGetFirst(final List<T> l) {
-        for ( RODRecordList value : map.values() ) {
+        return l.isEmpty() ? null : l.get(0);
-            if ( ! value.isEmpty() ) {
-                n++;
-            }
-        }
-        return n;
     }
 
-    // ------------------------------------------------------------------------------------------
-    //
-    //
-    // old style Generic accessors
-    //
-    // TODO -- DELETE ME
-    //
-    //
-    // ------------------------------------------------------------------------------------------
-
-    /**
-     * No-assumption version of getValues(name, class).  Returns Objects.
-     */
-    @Deprecated
-    public List<Object> getValues(final String name) {
-        return (List<Object>)(List)getValues(Feature.class, name);
-    }
-
-
-    // ------------------------------------------------------------------------------------------
-    //
-    //
-    // VariantContext helpers
-    //
-    //
-    // ------------------------------------------------------------------------------------------
-
     private <T extends Feature> List<T> addValues(final Collection<String> names,
                                                   final Class<T> type,
                                                   List<T> values,

public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.refdata.features;
 
 import net.sf.samtools.util.SequenceUtil;
+import org.broad.tribble.Feature;
 import org.broad.tribble.annotation.Strand;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.utils.Utils;
@@ -58,12 +59,12 @@ public class DbSNPHelper {
         return dbsnp;
     }
 
-    public static String rsIDOfFirstRealSNP(List<Object> featureList) {
+    public static String rsIDOfFirstRealSNP(List<Feature> featureList) {
         if (featureList == null)
             return null;
 
         String rsID = null;
-        for ( Object d : featureList ) {
+        for ( Feature d : featureList ) {
             if ( d instanceof DbSNPFeature ) {
                 if ( DbSNPHelper.isSNP((DbSNPFeature)d) ) {
                     rsID = ((DbSNPFeature)d).getRsID();
@@ -80,12 +81,12 @@ public class DbSNPHelper {
         return rsID;
     }
 
-    public static String rsIDOfFirstRealIndel(List<Object> featureList) {
+    public static String rsIDOfFirstRealIndel(List<Feature> featureList) {
         if (featureList == null)
             return null;
 
         String rsID = null;
-        for ( Object d : featureList ) {
+        for ( Feature d : featureList ) {
             if ( d instanceof DbSNPFeature ) {
                 if ( DbSNPHelper.isIndel((DbSNPFeature) d) ) {
                     rsID = ((DbSNPFeature)d).getRsID();

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -133,7 +134,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         HashMap classToRecord = new HashMap<String, Class>();
         for (String name: this.getPluginsByName().keySet()) {
             FeatureCodec codec = this.createByName(name);
-            classToRecord.put(name, codec.getFeatureType());
+            classToRecord.put(name.toUpperCase(), codec.getFeatureType());
         }
         return classToRecord;
     }
@@ -142,10 +143,25 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         return getAvailableTrackNamesAndTypes().get(fileDescriptor.getType().toUpperCase());
     }
 
+    /**
+     * Returns the FeatureClass (BeagleFeature) produced by an RMDTriplet, or null
+     * if no such binding is found
+     *
+     * @param fileDescriptor
+     * @return
+     */
     public Class getFeatureClass(RMDTriplet fileDescriptor) {
         return getAvailableTrackNamesAndRecordTypes().get(fileDescriptor.getType().toUpperCase());
     }
 
+    /**
+     * Returns a list of the available tribble track names (vcf,dbsnp,etc) that we can load
+     * @return
+     */
+    public String getAvailableTribbleFeatureNames() {
+        return Utils.join(",", getAvailableTrackNamesAndRecordTypes().keySet());
+    }
+
     /**
      * create a RMDTrack of the specified type
      *

public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -61,11 +62,8 @@ public class PrintRODsWalker extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Iterator<GATKFeature> rods = tracker.getAllValuesAsGATKFeatures().iterator();
+        for ( Feature feature : tracker.getValues(Feature.class) ) {
-        while ( rods.hasNext() ) {
+            out.println(feature.toString());
-            Object rod = rods.next().getUnderlyingObject();
-            if (VariantContextAdaptors.canBeConvertedToVariantContext(rod) )
-                out.println(rod.toString());
         }
 
         return 1;

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -154,9 +155,9 @@ public class VariantAnnotatorEngine {
                 String rsID = null;
 
                 if (vc.isSNP())
-                    rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
+                    rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
                 else if (vc.isIndel())
-                    rsID = DbSNPHelper.rsIDOfFirstRealIndel(tracker.getValues(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
+                    rsID = DbSNPHelper.rsIDOfFirstRealIndel(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
                 infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null );
                 // annotate dbsnp id if available and not already there
                 if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) )

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java

@@ -22,6 +22,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
+import org.broad.tribble.Feature;
 import org.broad.tribble.bed.FullBEDFeature;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -92,7 +93,7 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
 
     private CallableLociWalker.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, String track) {
         //System.out.printf("tracker %s%n", tracker);
-        List<Object> bindings = tracker.getValues(track);
+        List<Feature> bindings = tracker.getValues(Feature.class, track);
         if ( bindings.size() != 1 || ! (bindings.get(0) instanceof FullBEDFeature)) {
             throw new UserException.MalformedFile(String.format("%s track isn't a properly formated CallableBases object!", track));
         }

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

@@ -116,12 +116,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         if ( genotypeFilterExps.size() > 0 )
             hInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, 1, VCFHeaderLineType.String, "Genotype-level filter"));
 
-        List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
+        if ( mask.isBound() ) {
-        for ( ReferenceOrderedDataSource source : dataSources ) {
+            hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
-            if ( source.getName().equals("mask") ) {
-                hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
-                break;
-            }
         }
 
         writer.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -36,7 +37,7 @@ public class CountIntervals extends RefWalker<Long, Long> {
             return null;
         }
 
-        List<Object> checkIntervals = tracker.getValues("check");
+        List<Feature> checkIntervals = tracker.getValues(Feature.class, "check");
         return (long) checkIntervals.size();
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java

@@ -1,155 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.qc;
-
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.io.*;
-import java.math.BigInteger;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-import java.util.Collection;
-import java.util.List;
-
-/**
- * a walker for validating (in the style of validating pile-up) the ROD system.
- */
-@Reference(window=@Window(start=-40,stop=40))
-public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
-
-    // the divider to use in some of the text output
-    private static final String DIVIDER = ",";
-
-    @Output
-    public PrintStream out;
-
-    @Argument(fullName="PerLocusEqual",required=false,doc="Should we check that all records at the same site produce equivilent variant contexts")
-    public boolean allRecordsVariantContextEquivalent = false;
-    
-    // used to calculate the MD5 of a file
-    MessageDigest digest = null;
-
-    // we sometimes need to know what rods the engine's seen
-    List<ReferenceOrderedDataSource> rodList;
-
-    /**
-     * emit the md5 sums for each of the input ROD files (will save up a lot of time if and when the ROD files change
-     * underneath us).
-     */
-    public void initialize() {
-        // setup the MD5-er
-        try {
-            digest = MessageDigest.getInstance("MD5");
-        } catch (NoSuchAlgorithmException e) {
-            throw new ReviewedStingException("Unable to find MD5 checksumer");
-        }
-        out.println("Header:");
-        // enumerate the list of ROD's we've loaded
-        rodList = this.getToolkit().getRodDataSources();
-        for (ReferenceOrderedDataSource rod : rodList) {
-            out.println(rod.getName() + DIVIDER + rod.getType());
-            out.println(rod.getName() + DIVIDER + rod.getFile());
-            out.println(rod.getName() + DIVIDER + md5sum(rod.getFile()));
-        }
-        out.println("Data:");
-    }
-
-    /**
-     *
-     * @param tracker the ref meta data tracker to get RODs
-     * @param ref reference context
-     * @param context the reads
-     * @return an 1 for each site with a rod(s), 0 otherwise
-     */
-    @Override
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        int ret = 0;
-        if (tracker != null && tracker.getAllValuesAsGATKFeatures().size() > 0) {
-            out.print(context.getLocation() + DIVIDER);
-            Collection<GATKFeature> features = tracker.getAllValuesAsGATKFeatures();
-            for (GATKFeature feat : features)
-                out.print(feat.getName() + DIVIDER);
-            out.println(";");
-            ret++;
-        }
-
-        // if the argument was set, check for equivalence
-        if (allRecordsVariantContextEquivalent && tracker != null) {
-            Collection<VariantContext> col = tracker.getValues(VariantContext.class);
-            VariantContext con = null;
-            for (VariantContext contextInList : col)
-                if (con == null) con = contextInList;
-                else if (!con.equals(col)) out.println("FAIL: context " + col + " doesn't match " + con);
-        }
-        return ret;
-    }
-
-    /**
-     * Provide an initial value for reduce computations.
-     *
-     * @return Initial value of reduce.
-     */
-    @Override
-    public Integer reduceInit() {
-        return 0;
-    }
-
-    /**
-     * 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 value + sum;
-    }
-
-    @Override
-    public void onTraversalDone(Integer result) {
-        // Double check traversal result to make count is the same.
-        // TODO: Is this check necessary?
-        out.println("[REDUCE RESULT] Traversal result is: " + result);
-    }        
-
-    // shamelessly absconded and adapted from http://www.javalobby.org/java/forums/t84420.html
-    private String md5sum(File f) {
-        InputStream is;
-        try {
-            is = new FileInputStream(f);
-        } catch (FileNotFoundException e) {
-            return "Not a file";
-        }
-        byte[] buffer = new byte[8192];
-        int read = 0;
-        try {
-            while ((read = is.read(buffer)) > 0) {
-                digest.update(buffer, 0, read);
-            }
-            byte[] md5sum = digest.digest();
-            BigInteger bigInt = new BigInteger(1, md5sum);
-            return bigInt.toString(16);
-        }
-        catch (IOException e) {
-            throw new RuntimeException("Unable to process file for MD5", e);
-        }
-        finally {
-            try {
-                is.close();
-            }
-            catch (IOException e) {
-                throw new RuntimeException("Unable to close input stream for MD5 calculation", e);
-            }
-        }
-    }
-}

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -291,15 +290,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
      * @return Returns 1, but this value isn't used in the reduce step
      */
     public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-
         // If any ROD covers this site then we assume it is a site of known genetic variation and we skip it
-        boolean isSNP = false;
+        boolean isSNP = tracker.getNTracksWithBoundFeatures() > 0;
-        for( final GATKFeature rod : tracker.getAllValuesAsGATKFeatures() ) {
-            if( rod != null ) {
-                isSNP = true;
-                break;
-            }
-        }
         
         // Only use data from non-dbsnp sites
         // Assume every mismatch at a non-dbsnp site is indicative of poor quality

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
+import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.commandline.Argument;
@@ -140,7 +141,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         // get the RS IDs
         Set<String> rsIDs = null;
         if ( tracker.hasValues(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
-            List<Object> dbsnpList = tracker.getValues(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME);
+            List<Feature> dbsnpList = tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME);
             rsIDs = new HashSet<String>();
             for ( Object d : dbsnpList ) {
                 if (d instanceof DbSNPFeature )

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import net.sf.samtools.util.CloseableIterator;
+import org.broad.tribble.Feature;
 import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.commandline.Argument;
@@ -88,7 +89,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
             return 0;
 
-        String rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
+        String rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
 
         Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
 
@@ -117,7 +118,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
 
     private Collection<VariantContext> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref) {
         // we need to special case the HapMap format because indels aren't handled correctly
-        List<Object> features = tracker.getValues(variants.getName());
+        List<Feature> features = tracker.getValues(Feature.class, variants.getName());
         if ( features.size() > 0 && features.get(0) instanceof HapMapFeature ) {
             ArrayList<VariantContext> hapmapVCs = new ArrayList<VariantContext>(features.size());
             for ( Object feature : features ) {
@@ -223,7 +224,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                 samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
 
                 if ( samples.isEmpty() ) {
-                    List<Object> rods = tracker.getValues(variants.getName());
+                    List<Feature> rods = tracker.getValues(Feature.class, variants.getName());
                     if ( rods.size() == 0 )
                         throw new IllegalStateException("No rod data is present");
 

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

@@ -87,6 +87,13 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class UnknownTribbleType extends CommandLineException {
+        public UnknownTribbleType(String type, String message) {
+            super(String.format("Unknown tribble type %s: %s", type, message));
+        }
+    }
+
+
     public static class BadTmpDir extends UserException {
         public BadTmpDir(String message) {
             super(String.format("Failure working with the tmp directory %s. Override with -Djava.io.tmpdir=X on the command line to a bigger/better file system.  Exact error was %s", System.getProperties().get("java.io.tmpdir"), message));

public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java

@@ -154,7 +154,11 @@ public class ListFileUtils {
 
             // validate triplet type
             Class typeFromTribble = builderForValidation.getFeatureClass(triplet);
-            if ( typeFromTribble != null && ! rodBinding.getType().isAssignableFrom(typeFromTribble) )
+            if ( typeFromTribble == null )
+                throw new UserException.UnknownTribbleType(rodBinding.getTribbleType(),
+                        String.format("Field %s had provided type %s but there's no such Tribble type.  Available types are %s",
+                                rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.getAvailableTribbleFeatureNames()));
+            if ( ! rodBinding.getType().isAssignableFrom(typeFromTribble) )
                 throw new UserException.BadArgumentValue(rodBinding.getName(),
                         String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s",
                                 rodBinding.getName(), rodBinding.getType(), typeFromTribble));

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -42,28 +42,27 @@ import java.util.List;
  *
  */
 public class EngineFeaturesIntegrationTest extends WalkerTest {
-    private void testBadRODBindingInput(String type, String name) {
+    private void testBadRODBindingInput(String type, String name, Class c) {
         WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:" + type + " "
                 + b37dbSNP132 + " -R " + b37KGReference + " -o %s",
-                1, UserException.class);
+                1, c);
         executeTest(name, spec);
     }
 
-
     @Test() private void testBadRODBindingInputType1() {
-        testBadRODBindingInput("beagle", "BEAGLE input to VCF expecting walker");
+        testBadRODBindingInput("beagle", "BEAGLE input to VCF expecting walker", UserException.BadArgumentValue.class);
     }
 
     @Test() private void testBadRODBindingInputType2() {
-        testBadRODBindingInput("vcf3", "VCF3 input to VCF expecting walker");
+        testBadRODBindingInput("vcf3", "VCF3 input to VCF expecting walker", UserException.class);
     }
 
     @Test() private void testBadRODBindingInputType3() {
-        testBadRODBindingInput("bed", "Bed input to VCF expecting walker");
+        testBadRODBindingInput("bed", "Bed input to VCF expecting walker", UserException.BadArgumentValue.class);
     }
 
     @Test() private void testBadRODBindingInputTypeUnknownType() {
-        testBadRODBindingInput("bedXXX", "Unknown input to VCF expecting walker");
+        testBadRODBindingInput("bedXXX", "Unknown input to VCF expecting walker", UserException.UnknownTribbleType.class);
     }
 }
 

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
@@ -70,7 +71,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
         RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10), null);
-        Assert.assertEquals(tracker.getAllValuesAsGATKFeatures().size(), 0, "The tracker should not have produced any data");
+        Assert.assertEquals(tracker.getValues(Feature.class).size(), 0, "The tracker should not have produced any data");
     }
 
     /**

public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java

@@ -27,8 +27,6 @@ package org.broadinstitute.sting.gatk.refdata;
 import net.sf.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
-import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.commandline.Tags;
@@ -38,7 +36,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -173,7 +170,7 @@ public class RefMetaDataTrackerUnitTest {
     public void testRawBindings(MyTest test) {
         logger.warn("Testing " + test + " for number of bound tracks");
         RefMetaDataTracker tracker = test.makeTracker();
-        Assert.assertEquals(tracker.getNumberOfTracksWithValue(), test.nBoundTracks());
+        Assert.assertEquals(tracker.getNTracksWithBoundFeatures(), test.nBoundTracks());
 
         testSimpleBindings("A", tracker, test.AValues);
         testSimpleBindings("B", tracker, test.BValues);

public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java

@@ -26,7 +26,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
                  1,
-                 Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
+                 Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
         // TODO : Eric, update with new DBSNP

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java

@@ -14,13 +14,14 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 buildCommandLine(
                         "-T PhaseByTransmission",
+                        "-NO_HEADER",
                         "-R " + b37KGReference,
                         "-B:variant,VCF " + fundamentalTestVCF,
                         "-f NA12892+NA12891=NA12878",
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("45fef0e23113e2fcd9570379e2fc1b75")
+                Arrays.asList("")
         );
         executeTest("testBasicFunctionality", spec);
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java

@@ -18,7 +18,7 @@ public class ValidatingPileupIntegrationTest extends WalkerTest {
                 "-T ValidatingPileup" +
                 " -I " + validationDataLocation + "MV1994.selected.bam" +
                 " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
-                " -B:pileup,SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" +
+                " --pileup:SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" +
                 " -S SILENT -nt 8",0, Collections.<String>emptyList());
         executeTest("testEcoliThreaded",spec);
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java

@@ -19,8 +19,8 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
         String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
-        String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons -B:ValidateAlleles,VCF "+siteVCF+" -o %s";
+        String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
-        testArgs += " -B:ProbeIntervals,table "+intervalTable+" -BTI ProbeIntervals -B:MaskAlleles,VCF "+maskVCF;
+        testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("27f9450afa132888a8994167f0035fd7"));
@@ -32,8 +32,8 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
         String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
-        String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons -B:ValidateAlleles,VCF "+siteVCF+" -o %s";
+        String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
-        testArgs += " -B:ProbeIntervals,table "+intervalTable+" -BTI ProbeIntervals -B:MaskAlleles,VCF "+maskVCF;
+        testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30 --doNotUseBWA";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("f2611ff1d9cd5bedaad003251fed8bc1"));
@@ -45,8 +45,8 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
         String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
         String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
-        String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons -B:ValidateAlleles,VCF "+siteVCF+" -o %s";
+        String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
-        testArgs += " -B:ProbeIntervals,table "+intervalTable+" -BTI ProbeIntervals -B:MaskAlleles,VCF "+maskVCF;
+        testArgs += " --ProbeIntervals:table "+intervalTable+" -BTI ProbeIntervals --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30 --filterMonomorphic";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("77b3f30e38fedad812125bdf6cf3255f"));