Move additional VariantContext utility methods back to the GATK

Thanks to Eric for his feedback

protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java

@@ -320,7 +320,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         VariantContext subvc = vc.subContextFromSamples(samplesToPhase);
 //        logger.debug("original VC = " + vc);
 //        logger.debug("sub      VC = " + subvc);
-        return VariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF);
+        return GATKVariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF);
     }
 
     private List<VariantContext> processQueue(PhasingStats phaseStats, boolean processAll) {

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

@@ -280,7 +280,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
 
         if (multipleAllelesMergeType == GATKVariantContextUtils.MultipleAllelesMergeType.BY_TYPE) {
-            Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
+            Map<VariantContext.Type, List<VariantContext>> VCsByType = GATKVariantContextUtils.separateVariantContextsByType(vcs);
 
             // TODO -- clean this up in a refactoring
             // merge NO_VARIATION into another type of variant (based on the ordering in VariantContext.Type)
@@ -320,7 +320,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
             // re-compute chromosome counts
             VariantContextUtils.calculateChromosomeCounts(builder, false);
             if ( minimalVCF )
-                VariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
+                GATKVariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
             vcfWriter.add(builder.make());
         }
 

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

@@ -25,11 +25,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
-import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.vcf.VCFHeader;
 
@@ -277,8 +275,8 @@ public class ConcordanceMetrics {
             if ( truth.isMonomorphicInSamples() )
                 return EVAL_ONLY;
 
-            boolean evalSubsetTruth = VariantContextUtils.allelesAreSubset(eval,truth);
+            boolean evalSubsetTruth = GATKVariantContextUtils.allelesAreSubset(eval, truth);
-            boolean truthSubsetEval = VariantContextUtils.allelesAreSubset(truth,eval);
+            boolean truthSubsetEval = GATKVariantContextUtils.allelesAreSubset(truth, eval);
 
             if ( evalSubsetTruth && truthSubsetEval )
                 return ALLELES_MATCH;

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

@@ -44,6 +44,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@@ -246,7 +247,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
             vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
         }
 
-        vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
+        vc = GATKVariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
         vcfwriter.add(vc);
     }
 

public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java

@@ -50,6 +50,7 @@ public class GATKVariantContextUtils {
     public final static String MERGE_FILTER_IN_ALL = "FilteredInAll";
     public final static String MERGE_INTERSECTION = "Intersection";
 
+
     public enum GenotypeMergeType {
         /**
          * Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
@@ -1013,6 +1014,124 @@ public class GATKVariantContextUtils {
         }
     }
 
+    private final static Map<String, Object> subsetAttributes(final CommonInfo igc, final Collection<String> keysToPreserve) {
+        Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size());
+        for ( final String key : keysToPreserve  ) {
+            if ( igc.hasAttribute(key) )
+                attributes.put(key, igc.getAttribute(key));
+        }
+        return attributes;
+    }
+
+    /**
+     * @deprecated use variant context builder version instead
+     * @param vc                  the variant context
+     * @param keysToPreserve      the keys to preserve
+     * @return a pruned version of the original variant context
+     */
+    @Deprecated
+    public static VariantContext pruneVariantContext(final VariantContext vc, Collection<String> keysToPreserve ) {
+        return pruneVariantContext(new VariantContextBuilder(vc), keysToPreserve).make();
+    }
+
+    public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder, Collection<String> keysToPreserve ) {
+        final VariantContext vc = builder.make();
+        if ( keysToPreserve == null ) keysToPreserve = Collections.emptyList();
+
+        // VC info
+        final Map<String, Object> attributes = subsetAttributes(vc.getCommonInfo(), keysToPreserve);
+
+        // Genotypes
+        final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
+        for ( final Genotype g : vc.getGenotypes() ) {
+            final GenotypeBuilder gb = new GenotypeBuilder(g);
+            // remove AD, DP, PL, and all extended attributes, keeping just GT and GQ
+            gb.noAD().noDP().noPL().noAttributes();
+            genotypes.add(gb.make());
+        }
+
+        return builder.genotypes(genotypes).attributes(attributes);
+    }
+
+    public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) {
+        // if all alleles of vc1 are a contained in alleles of vc2, return true
+        if (!vc1.getReference().equals(vc2.getReference()))
+            return false;
+
+        for (Allele a :vc1.getAlternateAlleles()) {
+            if (!vc2.getAlternateAlleles().contains(a))
+                return false;
+        }
+
+        return true;
+    }
+
+    public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType(Collection<VariantContext> VCs) {
+        HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<VariantContext.Type, List<VariantContext>>();
+        for ( VariantContext vc : VCs ) {
+
+            // look at previous variant contexts of different type. If:
+            // a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
+            // b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list)
+            // c) neither: do nothing, just add vc to its own list
+            boolean addtoOwnList = true;
+            for (VariantContext.Type type : VariantContext.Type.values()) {
+                if (type.equals(vc.getType()))
+                    continue;
+
+                if (!mappedVCs.containsKey(type))
+                    continue;
+
+                List<VariantContext> vcList = mappedVCs.get(type);
+                for (int k=0; k <  vcList.size(); k++) {
+                    VariantContext otherVC = vcList.get(k);
+                    if (allelesAreSubset(otherVC,vc)) {
+                        // otherVC has a type different than vc and its alleles are a subset of vc: remove otherVC from its list and add it to vc's type list
+                        vcList.remove(k);
+                        // avoid having empty lists
+                        if (vcList.size() == 0)
+                            mappedVCs.remove(type);
+                        if ( !mappedVCs.containsKey(vc.getType()) )
+                            mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
+                        mappedVCs.get(vc.getType()).add(otherVC);
+                        break;
+                    }
+                    else if (allelesAreSubset(vc,otherVC)) {
+                        // vc has a type different than otherVC and its alleles are a subset of VC: add vc to otherVC's type list and don't add to its own
+                        mappedVCs.get(type).add(vc);
+                        addtoOwnList = false;
+                        break;
+                    }
+                }
+            }
+            if (addtoOwnList) {
+                if ( !mappedVCs.containsKey(vc.getType()) )
+                    mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
+                mappedVCs.get(vc.getType()).add(vc);
+            }
+        }
+
+        return mappedVCs;
+    }
+
+    public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) {
+        if ( allowedAttributes == null )
+            return vc;
+
+        GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
+        for ( final Genotype genotype : vc.getGenotypes() ) {
+            Map<String, Object> attrs = new HashMap<String, Object>();
+            for ( Map.Entry<String, Object> attr : genotype.getExtendedAttributes().entrySet() ) {
+                if ( allowedAttributes.contains(attr.getKey()) )
+                    attrs.put(attr.getKey(), attr.getValue());
+            }
+            newGenotypes.add(new GenotypeBuilder(genotype).attributes(attrs).make());
+        }
+
+        return new VariantContextBuilder(vc).genotypes(newGenotypes).make();
+    }
+
+
     private static class AlleleMapper {
         private VariantContext vc = null;
         private Map<Allele, Allele> map = null;

public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java

@@ -625,6 +625,10 @@ public class VariantContext implements Feature { // to enable tribble integratio
     public double getAttributeAsDouble(String key, double  defaultValue)  { return commonInfo.getAttributeAsDouble(key, defaultValue); }
     public boolean getAttributeAsBoolean(String key, boolean  defaultValue)  { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
 
+    public CommonInfo getCommonInfo() {
+        return commonInfo;
+    }
+
     // ---------------------------------------------------------------------------------------------------------
     //
     // Working with alleles

public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java

@@ -316,106 +316,6 @@ public class VariantContextUtils {
         return r;
     }
 
-    private final static Map<String, Object> subsetAttributes(final CommonInfo igc, final Collection<String> keysToPreserve) {
-        Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size());
-        for ( final String key : keysToPreserve  ) {
-            if ( igc.hasAttribute(key) )
-                attributes.put(key, igc.getAttribute(key));
-        }
-        return attributes;
-    }
-
-    /**
-     * @deprecated use variant context builder version instead
-     * @param vc                  the variant context
-     * @param keysToPreserve      the keys to preserve
-     * @return a pruned version of the original variant context
-     */
-    @Deprecated
-    public static VariantContext pruneVariantContext(final VariantContext vc, Collection<String> keysToPreserve ) {
-        return pruneVariantContext(new VariantContextBuilder(vc), keysToPreserve).make();
-    }
-
-    public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder, Collection<String> keysToPreserve ) {
-        final VariantContext vc = builder.make();
-        if ( keysToPreserve == null ) keysToPreserve = Collections.emptyList();
-
-        // VC info
-        final Map<String, Object> attributes = subsetAttributes(vc.commonInfo, keysToPreserve);
-
-        // Genotypes
-        final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
-        for ( final Genotype g : vc.getGenotypes() ) {
-            final GenotypeBuilder gb = new GenotypeBuilder(g);
-            // remove AD, DP, PL, and all extended attributes, keeping just GT and GQ
-            gb.noAD().noDP().noPL().noAttributes();
-            genotypes.add(gb.make());
-        }
-
-        return builder.genotypes(genotypes).attributes(attributes);
-    }
-
-    public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) {
-        // if all alleles of vc1 are a contained in alleles of vc2, return true
-        if (!vc1.getReference().equals(vc2.getReference()))
-            return false;
-
-        for (Allele a :vc1.getAlternateAlleles()) {
-            if (!vc2.getAlternateAlleles().contains(a))
-                return false;
-        }
-
-        return true;
-    }
-
-    public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType(Collection<VariantContext> VCs) {
-        HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<VariantContext.Type, List<VariantContext>>();
-        for ( VariantContext vc : VCs ) {
-
-            // look at previous variant contexts of different type. If:
-            // a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
-            // b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list)
-            // c) neither: do nothing, just add vc to its own list
-            boolean addtoOwnList = true;
-            for (VariantContext.Type type : VariantContext.Type.values()) {
-                if (type.equals(vc.getType()))
-                    continue;
-
-                if (!mappedVCs.containsKey(type))
-                    continue;
-
-                List<VariantContext> vcList = mappedVCs.get(type);
-                for (int k=0; k <  vcList.size(); k++) {
-                    VariantContext otherVC = vcList.get(k);
-                    if (allelesAreSubset(otherVC,vc)) {
-                        // otherVC has a type different than vc and its alleles are a subset of vc: remove otherVC from its list and add it to vc's type list
-                        vcList.remove(k);
-                        // avoid having empty lists
-                        if (vcList.size() == 0)
-                            mappedVCs.remove(type);
-                        if ( !mappedVCs.containsKey(vc.getType()) )
-                            mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
-                        mappedVCs.get(vc.getType()).add(otherVC);
-                        break;
-                    }
-                    else if (allelesAreSubset(vc,otherVC)) {
-                        // vc has a type different than otherVC and its alleles are a subset of VC: add vc to otherVC's type list and don't add to its own
-                        mappedVCs.get(type).add(vc);
-                        addtoOwnList = false;
-                        break;
-                    }
-                }
-            }
-            if (addtoOwnList) {
-                if ( !mappedVCs.containsKey(vc.getType()) )
-                    mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
-                mappedVCs.get(vc.getType()).add(vc);
-            }
-        }
-
-        return mappedVCs;
-    }
-
     //    TODO: remove that after testing
 //    static private void verifyUniqueSampleNames(Collection<VariantContext> unsortedVCs) {
 //        Set<String> names = new HashSet<String>();
@@ -431,23 +331,6 @@ public class VariantContextUtils {
 //    }
 
 
-    public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) {
-        if ( allowedAttributes == null )
-            return vc;
-
-        GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
-        for ( final Genotype genotype : vc.getGenotypes() ) {
-            Map<String, Object> attrs = new HashMap<String, Object>();
-            for ( Map.Entry<String, Object> attr : genotype.getExtendedAttributes().entrySet() ) {
-                if ( allowedAttributes.contains(attr.getKey()) )
-                    attrs.put(attr.getKey(), attr.getValue());
-            }
-            newGenotypes.add(new GenotypeBuilder(genotype).attributes(attrs).make());
-        }
-
-        return new VariantContextBuilder(vc).genotypes(newGenotypes).make();
-    }
-
     public static int getSize( VariantContext vc ) {
         return vc.getEnd() - vc.getStart() + 1;
     }