Adding pairwise AF table. Not polished at all, but usable none-the-less.

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java

@@ -31,10 +31,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
@@ -90,7 +90,59 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
     @DataPoint(description = "Multi-allelic Indel Novelty Rate")
     public String indelNoveltyRate = "NA";
 
-    // TODO -- Also, AF distributions (pairwise like TiTv)
+    @DataPoint(description="Histogram of allele frequencies")
+    AFHistogram AFhistogram = new AFHistogram();
+
+    /*
+     * AF histogram table object
+     */
+    static class AFHistogram implements TableType {
+        private Object[] colKeys, rowKeys = {"pairwise_AF"};
+        private int[] AFhistogram;
+
+        private static final double AFincrement = 0.01;
+        private static final int numBins = (int)(1.00 / AFincrement);
+
+        public AFHistogram() {
+            colKeys = initColKeys();
+            AFhistogram = new int[colKeys.length];
+        }
+
+        public Object[] getColumnKeys() {
+            return colKeys;
+        }
+
+        public Object[] getRowKeys() {
+            return rowKeys;
+        }
+
+        public Object getCell(int row, int col) {
+            return AFhistogram[col];
+        }
+
+        private static Object[] initColKeys() {
+            ArrayList<String> keyList = new ArrayList<String>(numBins + 1);
+            for ( double a = 0.00; a <= 1.01; a += AFincrement ) {
+                keyList.add(String.format("%.2f", a));
+            }
+            return keyList.toArray();
+        }
+
+        public String getName() { return "AFHistTable"; }
+
+        public void update(VariantContext vc) {
+            final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
+            if ( obj == null || !(obj instanceof List) )
+                return;
+
+            List<String> list = (List<String>)obj;
+            for ( String str : list ) {
+                final double AF = Double.valueOf(str);
+                final int bin = (int)(numBins * MathUtils.round(AF, 2));
+                AFhistogram[bin]++;
+            }
+        }
+    }
 
     public void initialize(VariantEvalWalker walker) {}
 
@@ -104,7 +156,6 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
         nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
     }
 
-
     public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( eval == null || eval.isMonomorphicInSamples() )
             return null;
@@ -129,6 +180,7 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
             default:
                 throw new UserException.BadInput("Unexpected variant context type: " + eval);
         }
+        AFhistogram.update(eval);
         
         return null; // we don't capture any interesting sites
     }