A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2320 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java

@@ -90,19 +90,19 @@ public abstract class ChipConcordance extends BasicVariantAnalysis {
 
         // don't procede if we have no truth data and no call
         if ( eval != null || chips.size() > 0 )
-            inc(chips, eval, ref);
+            return inc(chips, eval, ref);
-
+        else
             return null;
     }
 
-    public void inc(Map<String, Genotype> chips, Variation eval, char ref) {
+    public String inc(Map<String, Genotype> chips, Variation eval, char ref) {
 
         // each implementing class can decide whether the Variation is valid
         assertVariationIsValid(eval);
 
         // This shouldn't happen, but let's check anyways to be safe
         if (BaseUtils.simpleBaseToBaseIndex(ref) == -1)
-            return;
+            return null;
 
         // create a hash of samples to their Genotypes
         List<Genotype> evals = (eval != null ? ((VariantBackedByGenotype)eval).getGenotypes() : new ArrayList<Genotype>());
@@ -124,12 +124,17 @@ public abstract class ChipConcordance extends BasicVariantAnalysis {
         }
 
         // now we can finally update our truth tables with the truth vs. calls data
+        StringBuilder s = new StringBuilder();
         for (int i = 0; i < truthTables.length; i++) {
             if ( chipEvals[i] != null ) {
                 ConcordanceTruthTable table = truthTables[i];
-                table.addEntry(chipEvals[i], eval, ref);
+                String x = table.addEntry(chipEvals[i], eval, ref);
+                if ( x != null ) s.append(x);
             }
         }
+
+        String toReturn = s.toString();
+        return toReturn.equals("") ? null : toReturn;
     }
 
     public List<String> done() {

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java

@@ -17,7 +17,6 @@ import java.util.*;
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
 public class ConcordanceTruthTable {
-
     private static final int TRUE_POSITIVE = 0;
     private static final int TRUE_NEGATIVE = 1;
     private static final int FALSE_POSITIVE = 2;
@@ -83,7 +82,8 @@ public class ConcordanceTruthTable {
         // System.out.println("Table Size: "+table.length+" by "+table[1].length);
     }
 
-    public void addEntry(List<Pair<Genotype, Genotype>> chipEvals, Variation eval, char ref) {
+    public String addEntry(List<Pair<Genotype, Genotype>> chipEvals, Variation eval, char ref) {
+        String violation = null;
 
         // if the table represents a single sample, then we can calculate genotype stats
         if ( singleSampleMode ) {
@@ -114,7 +114,13 @@ public class ConcordanceTruthTable {
 
             int callType = getCallIndex(eval,ref);
 
-            addFrequencyEntry( truthType,callType,poolVariant.getSecond().getFirst() );
+            int numTrueSupportingAlleles = poolVariant.getSecond().getFirst();
+            if ( numTrueSupportingAlleles > 0 && truthType == VARIANT && callType != VARIANT ) {
+                violation = String.format("False negative: %s with %d alt alleles",
+                        chipEvals.get(0).getFirst(), numTrueSupportingAlleles);
+            }
+
+            addFrequencyEntry( truthType,callType, poolVariant.getSecond().getFirst() );
 
         }
 
@@ -122,6 +128,7 @@ public class ConcordanceTruthTable {
         // TODO -- You'll want to use eval and the chips from chipEvals (these are the first members of the pair)
         // TODO -- You'll also need to declare (and initialize) the relevant data arrays for the data
         // TODO -- Indexes like TRUE_POSITIVE are defined above for you
+        return violation;
     }
 
     public Pair< Genotype , Pair<Integer,Integer> > getPooledAlleleFrequency( List<Pair<Genotype,Genotype>> chips, char ref) {

java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java

@@ -168,4 +168,7 @@ public class BasicGenotype implements Genotype {
         return builder.toString();
     }
 
+    public String toString() {
+        return String.format("[%s %s]", getLocation(), getBases());   
+    }
 }