Added in an eval module that calculates the dispersion histograms between eval and comp (e.g. M_{i,j} = # of times eval observed to have AC i, comp AC j -- for af it's i/100 vs j/100 )

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4507 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java

@@ -404,15 +404,15 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
     }
 
     private int getAC(VariantContext vc) {
-        if ( vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass().isAssignableFrom(List.class) ) {
+        if ( List.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass()) ) {
             return ((List<Integer>) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY)).get(0);
-        } else if ( vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass().isAssignableFrom(Integer.class)) {
+        } else if ( Integer.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass())) {
             return (Integer) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY);
-        } else if ( vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass().isAssignableFrom(String.class)) {
+        } else if ( String.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass()) ) {
             // two ways of parsing
             String ac = (String) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY);
             if ( ac.startsWith("[") ) {
-                return Integer.parseInt(ac.replaceAll("[","").replaceAll("]",""));
+                return Integer.parseInt(ac.replaceAll("\\[","").replaceAll("\\]",""));
             } else {
                 try {
                     return Integer.parseInt(ac);
@@ -421,7 +421,7 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
                 }
             }
         } else {
-            throw new UserException(String.format("The format of the AC field does not appear to be of integer-list or String format"));
+            throw new UserException(String.format("The format of the AC field does not appear to be of integer-list or String format, class was %s",vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass()));
         }
     }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AlleleFrequencyComparison.java

@@ -0,0 +1,134 @@
+package org.broadinstitute.sting.gatk.walkers.varianteval;
+
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.report.tags.Analysis;
+import org.broadinstitute.sting.utils.report.tags.DataPoint;
+import org.broadinstitute.sting.utils.report.utils.TableType;
+
+import java.util.List;
+
+/**
+ *
+ */
+
+@Analysis(name = "Allele Frequency Comparison", description = "Compare allele frequency and counts between eval and comp")
+public class AlleleFrequencyComparison extends VariantEvaluator {
+    private static int MAX_AC_COUNT = 100; // todo -- command line argument?
+
+    @DataPoint(description="Counts of eval frequency versus comp frequency")
+    AFTable afTable = new AFTable();
+
+    @DataPoint(description="Counts of eval AC versus comp AC")
+    ACTable acTable = new ACTable(MAX_AC_COUNT);
+
+    public boolean enabled() { return true; }
+
+    public int getComparisonOrder() { return 2; }
+
+    public String getName() { return "Allele Frequency Comparison"; }
+
+    public AlleleFrequencyComparison(VariantEvalWalker parent) {
+        super(parent);
+    }
+
+    public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
+        if ( ! (isValidVC(eval) && isValidVC(comp))  ) {
+            return null;
+        } else {
+            afTable.update(getAF(eval),getAF(comp));
+            acTable.update(getAC(eval),getAC(comp));
+        }
+
+        return null; // there is nothing interesting
+    }
+
+    private static boolean isValidVC(final VariantContext vc) {
+        return (vc != null && !vc.isFiltered() && vc.getAlternateAlleles().size() == 1 && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY));
+    }
+
+    private static double getAF(VariantContext vc) {
+        return ((List<Double>) vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)).get(0);
+    }
+
+    private static int getAC(VariantContext vc) {
+        return ((List<Integer>) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY)).get(0);
+    }
+}
+
+class AFTable implements TableType {
+
+    protected int[][] afCounts = new int[101][101];
+
+    public Object[] getRowKeys() {
+        String[] afKeys = new String[101];
+        for ( int f = 0; f < 101; f ++ ) {
+            afKeys[f] = String.format("%.2f",(f+0.0)/100.0);
+        }
+
+        return afKeys;
+    }
+
+    public Object[] getColumnKeys() {
+        return getRowKeys(); // nice thing about symmetric tables
+    }
+
+    public Object getCell(int i, int j) {
+        return afCounts[i][j];
+    }
+
+    public String getName() {
+        return "Allele Frequency Concordance";
+    }
+
+    public void update(double eval, double comp) {
+        afCounts[af2index(eval)][af2index(comp)]++;
+    }
+
+    private int af2index(double d) {
+        return (int) Math.round(100*d);
+    }
+}
+
+class ACTable implements TableType {
+    protected int[][] acCounts;
+    protected int maxAC;
+
+    public ACTable(int acMaximum) {
+        maxAC = acMaximum;
+        acCounts = new int[acMaximum+1][acMaximum+1];
+    }
+
+    public Object[] getRowKeys() {
+        String[] acKeys = new String[maxAC+1];
+        for ( int i = 0 ; i <= maxAC ; i ++ ) {
+            acKeys[i] = String.format("%d",i);
+        }
+
+        return acKeys;
+    }
+
+    public Object[] getColumnKeys() {
+        return getRowKeys();
+    }
+
+    public Object getCell(int i, int j) {
+        return acCounts[i][j];
+    }
+
+    public String getName() {
+        return "Allele Counts Concordance";
+    }
+
+    public void update(int eval, int comp) {
+        eval = eval > maxAC ? maxAC : eval;
+        comp = comp > maxAC ? maxAC : comp;
+
+        acCounts[eval][comp]++;
+    }
+
+}