From 1bc5c7e99b2f78cb3b0adead515ccc313a360d0f Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 18 Feb 2011 04:02:14 +0000
Subject: [PATCH] boneheaded mistake, mixed up my min and max

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5271 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/annotator/HomopolymerRun.java     | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index bf02e816a..57557f6f5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -27,7 +27,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
 
         int run;
         if ( vc.isSNP() ) {
-            run = computeHomopolymerRun(vc.getAlternateAllele(0).getBases()[0], ref, true);
+            run = computeHomopolymerRun(vc.getAlternateAllele(0).getBases()[0], ref);
         } else if ( vc.isIndel() && ANNOTATE_INDELS ) {
             run = computeIndelHomopolymerRun(vc,ref);
         } else {
@@ -45,7 +45,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
 
     public boolean useZeroQualityReads() { return false; }
 
-    private static int computeHomopolymerRun(byte altAllele, ReferenceContext ref, boolean domin) {
+    private static int computeHomopolymerRun(byte altAllele, ReferenceContext ref) {
 
         // TODO -- this needs to be computed in a more accurate manner
         // We currently look only at direct runs of the alternate allele adjacent to this position
@@ -70,11 +70,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
             rightRun++;
         }
 
-        if (domin)
-            return Math.min(leftRun, rightRun);
-        else
-            return Math.max(leftRun, rightRun);
-
+        return Math.max(leftRun, rightRun);
      }
 
     private static int computeIndelHomopolymerRun(VariantContext vc, ReferenceContext ref) {
@@ -91,7 +87,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
                 }
             }
 
-            return computeHomopolymerRun(dBase, ref, false); // do max in both directions
+            return computeHomopolymerRun(dBase, ref);
         } else {
             // check that inserted bases are the same
             byte insBase = vc.getAlternateAllele(0).getBases()[0];
@@ -101,7 +97,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
                 }
             }
 
-            return computeHomopolymerRun(insBase,ref, false);
+            return computeHomopolymerRun(insBase,ref);
         }
     }
 }
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