Cleanup of codec locations. No more dbSNPHelper

-- refdata/features now in utils/codecs with the other codecs
-- Deleted dbsnpHelper.  rsID function now in VCFutils.  Remaining code either deleted or put into VariantContextAdaptors
-- Many associated import updates due to code move

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

@@ -1,10 +1,11 @@
 package org.broadinstitute.sting.gatk.refdata;
 
+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.broad.tribble.gelitext.GeliTextFeature;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@@ -92,6 +93,67 @@ public class VariantContextAdaptors {
     // --------------------------------------------------------------------------------------------------------------
 
     private static class DBSnpAdaptor implements VCAdaptor {
+        private static boolean isSNP(DbSNPFeature feature) {
+            return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
+        }
+
+        private static boolean isMNP(DbSNPFeature feature) {
+            return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
+        }
+
+        private static boolean isInsertion(DbSNPFeature feature) {
+            return feature.getVariantType().contains("insertion");
+        }
+
+        private static boolean isDeletion(DbSNPFeature feature) {
+            return feature.getVariantType().contains("deletion");
+        }
+
+        private static boolean isIndel(DbSNPFeature feature) {
+            return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature);
+        }
+
+        public static boolean isComplexIndel(DbSNPFeature feature) {
+            return feature.getVariantType().contains("in-del");
+        }
+
+        /**
+         * gets the alternate alleles.  This method should return all the alleles present at the location,
+         * NOT including the reference base.  This is returned as a string list with no guarantee ordering
+         * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
+         * frequency).
+         *
+         * @return an alternate allele list
+         */
+        public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
+            List<String> ret = new ArrayList<String>();
+            for (String allele : getAlleleList(feature))
+                if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
+            return ret;
+        }
+
+        /**
+         * gets the alleles.  This method should return all the alleles present at the location,
+         * including the reference base.  The first allele should always be the reference allele, followed
+         * by an unordered list of alternate alleles.
+         *
+         * @return an alternate allele list
+         */
+        public static List<String> getAlleleList(DbSNPFeature feature) {
+            List<String> alleleList = new ArrayList<String>();
+            // add ref first
+            if ( feature.getStrand() == Strand.POSITIVE )
+                alleleList = Arrays.asList(feature.getObserved());
+            else
+                for (String str : feature.getObserved())
+                    alleleList.add(SequenceUtil.reverseComplement(str));
+            if ( alleleList.size() > 0 && alleleList.contains(feature.getNCBIRefBase())
+                    && !alleleList.get(0).equals(feature.getNCBIRefBase()) )
+                Collections.swap(alleleList, alleleList.indexOf(feature.getNCBIRefBase()), 0);
+
+            return alleleList;
+        }
+
         /**
          * Converts non-VCF formatted dbSNP records to VariantContext. 
          * @return DbSNPFeature.
@@ -102,18 +164,18 @@ public class VariantContextAdaptors {
         @Override        
         public VariantContext convert(String name, Object input, ReferenceContext ref) {
             DbSNPFeature dbsnp = (DbSNPFeature)input;
-            if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
+            if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
                 return null;
-            Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true);
+            Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true);
 
-            if ( DbSNPHelper.isSNP(dbsnp) || DbSNPHelper.isIndel(dbsnp) || DbSNPHelper.isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
+            if ( isSNP(dbsnp) || isIndel(dbsnp) || isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
                 // add the reference allele
                 List<Allele> alleles = new ArrayList<Allele>();
                 alleles.add(refAllele);
 
                 // add all of the alt alleles
                 boolean sawNullAllele = refAllele.isNull();
-                for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
+                for ( String alt : getAlternateAlleleList(dbsnp) ) {
                     if ( ! Allele.acceptableAlleleBases(alt) ) {
                         //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
                         return null;

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

@@ -1,169 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.refdata.features;
-
-import net.sf.samtools.util.SequenceUtil;
-import org.broad.tribble.annotation.Strand;
-import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * this class contains static helper methods for DbSNP
- */
-public class DbSNPHelper {
-
-    private DbSNPHelper() {} // don't make a DbSNPHelper
-
-    public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
-        if ( VCs == null )
-            return null;
-
-        String rsID = null;
-        for ( VariantContext vc : VCs ) {
-            if ( vc.getType() == type ) {
-                rsID = vc.getID();
-                break;
-            }
-        }
-
-        return rsID;
-    }
-
-    /**
-     * get the -1 * (log 10 of the error value)
-     *
-     * @return the log based error estimate
-     */
-    public static double getNegLog10PError(DbSNPFeature feature) {
-        return 4; // -log10(0.0001)
-    }
-
-    //
-    // What kind of variant are we?
-    //
-    // ----------------------------------------------------------------------
-    public static boolean isSNP(DbSNPFeature feature) {
-        return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
-    }
-
-    public static boolean isMNP(DbSNPFeature feature) {
-        return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
-    }
-
-    public static String toMediumString(DbSNPFeature feature) {
-        String s = String.format("%s:%d:%s:%s", feature.getChr(), feature.getStart(), feature.getRsID(), Utils.join("",feature.getObserved()));
-        if (isSNP(feature)) s += ":SNP";
-        if (isIndel(feature)) s += ":Indel";
-        if (isHapmap(feature)) s += ":Hapmap";
-        if (is2Hit2Allele(feature)) s += ":2Hit";
-        return s;
-    }
-
-    public static boolean isInsertion(DbSNPFeature feature) {
-        return feature.getVariantType().contains("insertion");
-    }
-
-    public static boolean isDeletion(DbSNPFeature feature) {
-        return feature.getVariantType().contains("deletion");
-    }
-
-    public static boolean isIndel(DbSNPFeature feature) {
-        return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature);
-    }
-
-    public static boolean isComplexIndel(DbSNPFeature feature) {
-        return feature.getVariantType().contains("in-del");
-    }
-
-    public static boolean isHapmap(DbSNPFeature feature) {
-        return feature.getValidationStatus().contains("by-hapmap");
-    }
-
-    public static boolean is2Hit2Allele(DbSNPFeature feature) {
-        return feature.getValidationStatus().contains("by-2hit-2allele");
-    }
-
-    public static boolean is1000genomes(DbSNPFeature feature) {
-        return feature.getValidationStatus().contains("by-1000genomes");
-    }
-
-    public static boolean isMQ1(DbSNPFeature feature) {
-        return feature.getWeight() == 1;
-    }
-
-    /**
-     * gets the alternate alleles.  This method should return all the alleles present at the location,
-     * NOT including the reference base.  This is returned as a string list with no guarantee ordering
-     * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
-     * frequency).
-     *
-     * @return an alternate allele list
-     */
-    public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
-        List<String> ret = new ArrayList<String>();
-        for (String allele : getAlleleList(feature))
-            if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
-        return ret;
-    }
-
-    public static boolean onFwdStrand(DbSNPFeature feature) {
-        return feature.getStrand() == Strand.POSITIVE;
-    }
-
-    public static String getReference(DbSNPFeature feature) {
-        return feature.getNCBIRefBase();
-    }
-
-    public static String toSimpleString(DbSNPFeature feature) {
-        return String.format("%s:%s:%s", feature.getRsID(), feature.getObserved(), (feature.getStrand() == Strand.POSITIVE) ? "+" : "-");
-    }
-
-    /**
-     * gets the alleles.  This method should return all the alleles present at the location,
-     * including the reference base.  The first allele should always be the reference allele, followed
-     * by an unordered list of alternate alleles.
-     *
-     * @return an alternate allele list
-     */
-    public static List<String> getAlleleList(DbSNPFeature feature) {
-        List<String> alleleList = new ArrayList<String>();
-            // add ref first
-            if ( onFwdStrand(feature) )
-                alleleList = Arrays.asList(feature.getObserved());
-            else
-                for (String str : feature.getObserved())
-                    alleleList.add(SequenceUtil.reverseComplement(str));
-            if ( alleleList.size() > 0 && alleleList.contains(getReference(feature)) && !alleleList.get(0).equals(getReference(feature)) )
-                Collections.swap(alleleList, alleleList.indexOf(getReference(feature)), 0);
-
-        return alleleList;
-    }
-}

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

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
@@ -34,9 +33,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

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

@@ -29,15 +29,11 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -158,7 +154,7 @@ public class VariantAnnotatorEngine {
     private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
         for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
             if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
-                String rsID = DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
+                String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
                 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/beagle/BeagleOutputToVCFWalker.java

@@ -31,7 +31,7 @@ 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.features.beagle.BeagleFeature;
+import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;

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

@@ -32,8 +32,8 @@ 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.refdata.SeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java

@@ -39,9 +39,9 @@ import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.Transcript;
+import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;

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

@@ -32,7 +32,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.refdata.features.sampileup.SAMPileupFeature;
+import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java

@@ -14,9 +14,8 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.BaseUtils;

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

@@ -33,7 +33,6 @@ 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.refdata.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -120,7 +119,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
             return 0;
 
-        String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
+        String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
 
         Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
 

public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.beagle;
+package org.broadinstitute.sting.utils.codecs.beagle;
 /*
  * Copyright (c) 2010 The Broad Institute
  *

public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java

@@ -22,7 +22,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.gatk.refdata.features.beagle;
+package org.broadinstitute.sting.utils.codecs.beagle;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
 
-import org.apache.commons.io.filefilter.FalseFileFilter;
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;

public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java

@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.sampileup;
+package org.broadinstitute.sting.utils.codecs.sampileup;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
@@ -35,7 +35,7 @@ import java.util.ArrayList;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
+import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType;
 
 /**
  * A Tribble encoder / decoder for SAM pileup data. 

public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java

@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.sampileup;
+package org.broadinstitute.sting.utils.codecs.sampileup;
 
 import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;

public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java

@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.samread;
+package org.broadinstitute.sting.utils.codecs.samread;
 
 import net.sf.samtools.Cigar;
 import net.sf.samtools.TextCigarCodec;

public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java

@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.samread;
+package org.broadinstitute.sting.utils.codecs.samread;
 
 import org.broad.tribble.Feature;
 

public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;

public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.readers.LineReader;

public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.GenomeLoc;

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java

@@ -180,4 +180,19 @@ public class VCFUtils {
 
         return new HashSet<VCFHeaderLine>(map.values());
     }
+
+    public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
+        if ( VCs == null )
+            return null;
+
+        String rsID = null;
+        for ( VariantContext vc : VCs ) {
+            if ( vc.getType() == type ) {
+                rsID = vc.getID();
+                break;
+            }
+        }
+
+        return rsID;
+    }
 }

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

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broad.tribble.Feature;
-import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.testng.Assert;
@@ -35,7 +34,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import javax.script.Bindings;
 import java.util.List;
 import java.util.EnumSet;
 /**

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

@@ -10,7 +10,7 @@ import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java

@@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;

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

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;

public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java

@@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.features.table.BedTableCodec;
+import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;