Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval".

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1862 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -444,7 +444,7 @@ public class GenomeAnalysisEngine {
         // Check to see that no forbidden rods are present.
         for (ReferenceOrderedData<? extends ReferenceOrderedDatum> rod : rods) {
             if (!WalkerManager.isAllowed(walker, rod))
-                throw new ArgumentException(String.format("Walker does not allow access to metadata: %s.  If this is incorrect, change the @Allows metadata", rod.getName()));
+                throw new ArgumentException(String.format("Walker of type %s does not allow access to metadata: %s.  If this is incorrect, change the @Allows metadata", walker.getClass(), rod.getName()));
         }
     }
 

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

@@ -0,0 +1,56 @@
+package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+
+import java.util.List;
+import java.util.ArrayList;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: andrewk
+ * Date: Sep 30, 2009
+ * Time: 5:28:57 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+//  @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type= rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
+
+public class ValidationDataAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
+    private int calls_at_validated_sites = 0;
+    private int calls_at_sites_validated_true = 0;
+    private int validated_sites = 0;
+
+    public ValidationDataAnalysis() {
+        super("validation_data_analysis");
+    }
+
+    public String update(Variation eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
+
+        validated_sites++;
+        Variation val_data = (Variation) tracker.lookup("validation", null);
+        Variation dbsnp = (Variation) tracker.lookup("dbsnp",null);
+
+        if (eval != null) {
+            calls_at_sites_validated_true++;
+            //out.format("Has validaiton data: %s\n", val_data.getLocation());
+            if (val_data != null) {
+                //out.format("Validated true: %s\n", val_data.getLocation());
+                calls_at_validated_sites++;
+            }
+        }
+        out.println(context.getLocation());
+
+        return "";
+    }
+
+    public List<String> done() {
+        List<String> s = new ArrayList<String>();
+        s.add(String.format("validated sites               %d", validated_sites));
+        s.add(String.format("calls at validated sites      %d", calls_at_sites_validated_true));
+        s.add(String.format("calls at sites validated true %d", calls_at_validated_sites));
+        s.add(String.format("%% validated true             %f", (float) calls_at_validated_sites / calls_at_sites_validated_true));
+        return s;
+    }
+}

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

@@ -26,7 +26,7 @@ import java.util.*;
  *
  */
 @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change
-@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class)})
+@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
 public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     @Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
     public int minConfidenceScore = -1;
@@ -115,6 +115,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
         //
         // Add new analyses here!
         //
+        analyses.add(new ValidationDataAnalysis());
         analyses.add(new PooledGenotypeConcordance(pathToHapmapPoolFile));
         analyses.add(new VariantCounter());
         analyses.add(new VariantDBCoverage(knownSNPDBName));