From 8bc60eb792f377481bdc3485c8f3d0dcf0d1cc6d Mon Sep 17 00:00:00 2001
From: bbimber <M0ndayBlu>
Date: Wed, 12 Jun 2019 10:30:40 -0700
Subject: [PATCH] Refactor VariantEval methods to allow subclass to override

---
 .../tools/walkers/varianteval/VariantEval.java       |  8 ++++++--
 .../varianteval/evaluators/VariantEvaluator.java     |  4 ++++
 .../walkers/varianteval/util/EvaluationContext.java  | 12 +++++++++---
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
index 765e34fb0cd..3bdf0ebb40f 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
@@ -414,7 +414,7 @@ private void checkForIncompatibleEvaluatorsAndStratifiers( final List<VariantStr
             for ( Class<? extends VariantEvaluator> ec : evaluationClasses )
                 if ( vs.getIncompatibleEvaluators().contains(ec) )
                     throw new CommandLineException.BadArgumentValue("ST and ET",
-                            "The selected stratification " + vs.getName() + 
+                            "The selected stratification " + vs.getName() +
                                     " and evaluator " + ec.getSimpleName() +
                                     " are incompatible due to combinatorial memory requirements." +
                                     " Please disable one");
@@ -427,11 +427,15 @@ final void createStratificationStates(final List<VariantStratifier> stratificati
 
         logger.info("Creating " + stratManager.size() + " combinatorial stratification states");
         for ( int i = 0; i < stratManager.size(); i++ ) {
-            EvaluationContext ec = new EvaluationContext(this, evaluationObjects);
+            EvaluationContext ec = getEvaluationContext(evaluationObjects);
             stratManager.set(i, ec);
         }
     }
 
+    protected EvaluationContext getEvaluationContext(final Set<Class<? extends VariantEvaluator>> evaluationObjects) {
+        return new EvaluationContext(this, evaluationObjects);
+    }
+
     private class PositionAggregator {
         private SimpleInterval i = null;
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java
index e14398c9aec..020caf6394e 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -11,6 +11,10 @@ public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
     private VariantEval walker;
     private final String simpleName;
 
+    protected VariantEvaluator(String simpleName) {
+        this.simpleName = simpleName;
+    }
+
     protected VariantEvaluator() {
         this.simpleName = getClass().getSimpleName();
     }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
index 60b3656fcdf..11822151b37 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
@@ -10,13 +10,14 @@
 import org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager;
 
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
 
-public final class EvaluationContext {
+public class EvaluationContext {
     // NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function
     final VariantEval walker;
-    private final ArrayList<VariantEvaluator> evaluationInstances;
+    private final List<VariantEvaluator> evaluationInstances;
     private final Set<Class<? extends VariantEvaluator>> evaluationClasses;
 
     public EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
@@ -26,8 +27,11 @@ public EvaluationContext(final VariantEval walker, final Set<Class<? extends Var
     private EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses, final boolean doInitialize) {
         this.walker = walker;
         this.evaluationClasses = evaluationClasses;
-        this.evaluationInstances = new ArrayList<VariantEvaluator>(evaluationClasses.size());
+        this.evaluationInstances = initializeEvaluationInstances(doInitialize);
+    }
 
+    protected List<VariantEvaluator> initializeEvaluationInstances(boolean doInitialize) {
+        List<VariantEvaluator> ret = new ArrayList<>(evaluationClasses.size());
         for ( final Class<? extends VariantEvaluator> c : evaluationClasses ) {
             try {
                 final VariantEvaluator eval = c.newInstance();
@@ -39,6 +43,8 @@ private EvaluationContext(final VariantEval walker, final Set<Class<? extends Va
                 throw new GATKException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e);
             }
         }
+
+        return ret;
     }
 
     /**