oneoffs walker to assess GLs at truth sites

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5083 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessLikelihoodsAtTruth.java

@@ -0,0 +1,106 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.oneoffprojects.walkers;
+
+import org.broad.tribble.util.variantcontext.Genotype;
+import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
+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.RodWalker;
+import org.broadinstitute.sting.utils.MathUtils;
+
+import java.util.*;
+
+/**
+ * Assesses GLs at truth sites.
+ * Use -B:variant,vcf and -B:truth,vcf
+ */
+public class AssessLikelihoodsAtTruth extends RodWalker<Integer, Integer> {
+
+    private int[] nonErrors = new int[101];
+    private int[] observations = new int[101];
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null ) // RodWalkers can make funky map calls
+            return 0;
+
+        VariantContext variant = tracker.getVariantContext(ref, "variant", null, context.getLocation(), true);
+        if ( variant == null )
+            return 0;
+
+        VariantContext truth = tracker.getVariantContext(ref, "truth", null, context.getLocation(), true);
+        if ( truth == null )
+            return 0;
+
+        for ( Map.Entry<String, Genotype> GLgenotypeEntry : variant.getGenotypes().entrySet() ) {
+            Genotype GLgenotype = GLgenotypeEntry.getValue();
+            if ( GLgenotype.isNoCall() )
+                continue;
+
+            if ( !truth.hasGenotype(GLgenotypeEntry.getKey()) )
+                continue;
+
+            Genotype truthGenotype = truth.getGenotype(GLgenotypeEntry.getKey());
+            if ( truthGenotype.isNoCall() )
+                continue;
+
+            GenotypeLikelihoods GLs = GLgenotype.getLikelihoods();
+            if ( GLs == null ) {
+                logger.warn("There are no GLs at " + context.getLocation());
+                continue;
+            }
+
+            double[] normalizedGLs = MathUtils.normalizeFromLog10(GLs.getAsVector());
+            double myGL = GLgenotype.isHomRef() ? normalizedGLs[0] : (GLgenotype.isHet() ? normalizedGLs[1] : normalizedGLs[2]);
+            int roundedGL = (int)Math.round(100.0 * myGL);
+
+            observations[roundedGL]++;
+            boolean correctGenotype = GLgenotype.getType().equals(truthGenotype.getType());
+            if ( correctGenotype )
+                nonErrors[roundedGL]++;
+        }
+
+        return 1;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer counter, Integer sum) {
+        return counter + sum;
+    }
+
+    public void onTraversalDone(Integer sum) {
+        System.out.println("GL_probability\tone_minus_error_rate\tobservations");
+        for (int i = 0; i < 101; i++) {
+            if ( observations[i] > 0 )
+                System.out.println(String.format("%.2f\t%.2f\t%d", (double)i/100.0, (double)nonErrors[i]/(double)observations[i], observations[i]));
+        }
+    }
+}