From d573fc4adfd9f68921bdc413fc9afdd17333e5a2 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Wed, 23 Mar 2016 08:47:48 -0400
Subject: [PATCH] Add some comments to AFCalculationResult Add note that VC may
 be null (in this case because there are too many alts) Add todo for possible
 inefficient code

---
 .../gatk/tools/walkers/genotyper/GenotypingEngine.java        | 2 +-
 .../gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java | 2 +-
 .../tools/walkers/genotyper/afcalc/AFCalculationResult.java   | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
index 6c1b28cb2..91c27cdd0 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
@@ -521,7 +521,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
     @Ensures("MathUtils.goodLog10Probability(result)")
     protected final double estimateLog10ReferenceConfidenceForOneSample(final int depth, final double log10OfTheta) {
         final double log10PofNonRef = log10OfTheta + getRefBinomialProbLog10(depth);
-        return MathUtils.log10OneMinusX(Math.pow(10.0, log10PofNonRef));
+        return MathUtils.log10OneMinusX(Math.pow(10.0, log10PofNonRef));  //TODO: this 10^log(PofNonRef) seems inefficient
     }
 
     /**
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
index 7fcd452b3..6cde056c0 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
@@ -312,7 +312,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
      * Compute genotypes at a given locus.
      *
      * @param vc         the GL-annotated variant context
-     * @return the VariantCallContext object
+     * @return the VariantCallContext object (can be null)
      */
     public VariantCallContext calculateGenotypes(VariantContext vc) {
         final VariantContext.Type type = vc.getType();
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java
index 83ffa852c..c9665bf80 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java
@@ -69,8 +69,8 @@ import java.util.*;
  * that users of this code can rely on the values coming out of these functions.
  */
 public class AFCalculationResult {
-    private final static int AF0 = 0;
-    private final static int AF1p = 1;
+    private final static int AF0 = 0;  //index of the AC=0 entry in the log10 array (of priors, likelihoods, or posteriors listed below)
+    private final static int AF1p = 1;  //index of the AC>0 entry in the log10 array
     private final static int LOG_10_ARRAY_SIZES = 2;
 
     private final double[] log10LikelihoodsOfAC;