Bring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.

protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java

@@ -35,10 +35,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
@@ -52,12 +50,6 @@ import java.util.*;
  */
 public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
-    public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
-    public static final VCFInfoHeaderLine[] descriptions = {
-            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
-            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
-            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };
-
     private Set<String> founderIds = new HashSet<String>();
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
@@ -78,8 +70,8 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
     }
 
     public List<String> getKeyNames() {
-        return Arrays.asList(keyNames);
+        return Arrays.asList(ChromosomeCountConstants.keyNames);
     }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(descriptions); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(ChromosomeCountConstants.descriptions); }
 }

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

@@ -0,0 +1,44 @@
+/*
+ * 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.annotator;
+
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
+
+
+/**
+ * Keys and descriptions for the common chromosome count annotations
+ */
+public class ChromosomeCountConstants {
+
+    public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
+
+    public static final VCFInfoHeaderLine[] descriptions = {
+            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
+            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
+            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };
+}

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

@@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
+import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.variant.vcf.*;
@@ -217,7 +217,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
         if ( SET_KEY != null )
             headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants"));
         if ( !ASSUME_IDENTICAL_SAMPLES )
-             headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions));
+             headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
         VCFHeader vcfHeader = new VCFHeader(headerLines, samples);
         vcfHeader.setWriteCommandLine(!SUPPRESS_COMMAND_LINE_HEADER);
         vcfWriter.writeHeader(vcfHeader);