archiving, removing, or promoting to core from playground

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4134 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,75 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
-
-import org.broad.tribble.util.variantcontext.Allele;
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-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 org.broadinstitute.sting.commandline.Output;
-
-import java.util.EnumSet;
-import java.io.PrintStream;
-
-/**
- * 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> {
-    @Output
-    PrintStream out;
-
-    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(ref, "eval", vc, loc, true);
-                truth = tracker.getVariantContext(ref, "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);
-    }
-
-}