Added playground walker that does a basic concordance check between two VCF files - an eval and a truth file - across all samples in the eval file. Produces per-sample, per-locus debug info and simple concordance stats. This is not meant to be extended, but rather used for validating the HapMap to VCF conversion in preparation for retiring GFF-based HapMap data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2813 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/VCFConcordance.java

@@ -0,0 +1,73 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.EnumSet;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * Calculates concordance between two VCF files; used for testing conversion of HapMap data to VCF
+ */
+@Requires(value={DataSource.REFERENCE})
+public class VCFConcordance extends RodWalker<Integer, Integer> {
+
+    int correct = 0;
+    int incorrect = 0;
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if (tracker != null) {
+            EnumSet<VariantContext.Type> vc = EnumSet.of(VariantContext.Type.SNP);
+            GenomeLoc loc = context.getLocation();
+            VariantContext eval = null;
+            VariantContext truth = null;
+            try {
+                eval = tracker.getVariantContext("eval", vc, loc, true);
+                truth = tracker.getVariantContext("truth", vc, loc, true);
+            } catch (java.util.NoSuchElementException e) {
+                return 0;
+            }
+            assert(truth != null);
+            for (String eval_samplename : eval.getGenotypes().keySet()) {
+                Genotype eval_genotype = eval.getGenotype(eval_samplename);
+                if (truth.hasGenotype(eval_samplename) && eval.getAlleles() != Allele.NO_CALL) {
+                    Genotype truth_genotype = truth.getGenotype(eval_samplename);
+                    if (eval_genotype.sameGenotype(truth_genotype)) {
+                        out.printf("== ");
+                        correct++;
+                    }else{
+                        out.printf("<> ");
+                        incorrect++;
+                    }
+                    out.printf("%s %s %s %s\n", loc, eval_samplename, eval_genotype, truth_genotype);
+                }
+            }
+        }
+
+        return 1;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
+    }
+
+    public void onTraversalDone(Integer value) {
+        out.format("Correct:     %d\n", correct);
+        out.format("Incorrect:   %d\n", incorrect);
+        out.format("Concordance: %.1f\n", (float)correct/(correct+incorrect)*100);
+    }
+
+}