From b68d1ac2600d04fcd0cac9ff4da7c5950fd4216c Mon Sep 17 00:00:00 2001
From: James <emeryj@broadinstitute.org>
Date: Tue, 4 Dec 2018 12:39:39 -0500
Subject: [PATCH] responded to first round of comments

---
 .../htsjdk/variant/variantcontext/Genotype.java    | 14 +++++++-------
 .../variant/variantcontext/VariantContext.java     | 10 +++++++---
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/src/main/java/htsjdk/variant/variantcontext/Genotype.java b/src/main/java/htsjdk/variant/variantcontext/Genotype.java
index deb0e54efb..a0c80c2e22 100644
--- a/src/main/java/htsjdk/variant/variantcontext/Genotype.java
+++ b/src/main/java/htsjdk/variant/variantcontext/Genotype.java
@@ -202,28 +202,28 @@ protected GenotypeType determineType() {
         }
 
         boolean sawNoCall = false, sawMultipleAlleles = false;
-        Allele firstAllele = null;
+        Allele firstCallAllele = null;
 
         for ( int i = 0; i < alleles.size(); i++ ) {
             final Allele allele = alleles.get(i);
             if ( allele.isNoCall() ) {
                 sawNoCall = true;
-            } else if ( firstAllele == null ) {
-                firstAllele = allele;
-            } else if ( !allele.equals(firstAllele) )
+            } else if ( firstCallAllele == null ) {
+                firstCallAllele = allele;
+            } else if ( !allele.equals(firstCallAllele) )
                 sawMultipleAlleles = true;
         }
 
         if ( sawNoCall ) {
-            if ( firstAllele == null )
+            if ( firstCallAllele == null )
                 return GenotypeType.NO_CALL;
             return GenotypeType.MIXED;
         }
 
-        if ( firstAllele == null )
+        if ( firstCallAllele == null )
             throw new IllegalStateException("BUG: there are no alleles present in this genotype but the alleles list is not null");
 
-        return sawMultipleAlleles ? GenotypeType.HET : firstAllele.isReference() ? GenotypeType.HOM_REF : GenotypeType.HOM_VAR;
+        return sawMultipleAlleles ? GenotypeType.HET : firstCallAllele.isReference() ? GenotypeType.HOM_REF : GenotypeType.HOM_VAR;
     }
 
     /**
diff --git a/src/main/java/htsjdk/variant/variantcontext/VariantContext.java b/src/main/java/htsjdk/variant/variantcontext/VariantContext.java
index abc2c1e3c2..54bc38d73f 100644
--- a/src/main/java/htsjdk/variant/variantcontext/VariantContext.java
+++ b/src/main/java/htsjdk/variant/variantcontext/VariantContext.java
@@ -1353,8 +1353,11 @@ private void validateGenotypes() {
         if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null");
 
         for ( int i = 0; i < genotypes.size(); i++ ) {
-            if ( genotypes.get(i).isAvailable() ) {
-                for ( Allele gAllele : genotypes.get(i).getAlleles() ) {
+            Genotype genotype = genotypes.get(i);
+            if ( genotype.isAvailable() ) {
+                final List<Allele> alleles = genotype.getAlleles();
+                for ( int j = 0; j < alleles.size(); j++ ) {
+                    final Allele gAllele = alleles.get(j);
                     if ( ! hasAllele(gAllele) && gAllele.isCalled() )
                         throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
                 }
@@ -1698,7 +1701,8 @@ public boolean hasSymbolicAlleles() {
     }
 
     public static boolean hasSymbolicAlleles( final List<Allele> alleles ) {
-        for (int i = 0; i < alleles.size(); i++ ) {
+        int size = alleles.size();
+        for (int i = 0; i < size; i++ ) {
             if (alleles.get(i).isSymbolic()) {
                 return true;
             }