From 70f8ab6f89b10f2c6c06c21697113a805367d906 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 May 2011 15:22:50 +0000
Subject: [PATCH] Adding AF bin stratification for VariantEval.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5728 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../stratifications/AlleleFrequency.java      | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
new file mode 100755
index 000000000..0daad99dc
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
@@ -0,0 +1,41 @@
+package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
+
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.MathUtils;
+
+import java.util.ArrayList;
+import java.util.Set;
+
+public class AlleleFrequency extends VariantStratifier {
+    // needs to know the variant context
+    private ArrayList<String> states;
+
+    @Override
+    public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames, Set<String> contigNames) {
+        states = new ArrayList<String>();
+        for( double a = 0.000; a <= 1.005; a += 0.005 ) {
+            states.add(String.format("%.3f", a));
+        }
+    }
+
+    public ArrayList<String> getAllStates() {
+        return states;
+    }
+
+    public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+        ArrayList<String> relevantStates = new ArrayList<String>();
+
+        if (eval != null) {
+            try {
+                relevantStates.add(String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF") / 5.0, 3))));
+            } catch (Exception e) {
+                return relevantStates;
+            }
+        }
+
+        return relevantStates;
+    }
+}