From 913c8b231fddeebcda205e9c88489b3f1876a1ea Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 27 Mar 2012 10:34:56 -0400
Subject: [PATCH] Fix ErrorRatePerCycle to overload equals and hashcode

-- Fixes failing integration tests
---
 .../diagnostics/ErrorRatePerCycle.java        | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
index e7a2f74e2..10ac523e6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
@@ -91,6 +91,25 @@ public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
             this.cycle = cycle;
         }
 
+        // Must overload hashCode and equals to properly work with GATKReportColumn
+        @Override
+        public int hashCode() {
+            return readGroup.hashCode() + 33 * cycle;
+        }
+
+        @Override
+        public boolean equals(final Object o) {
+            if (this == o) return true;
+            if (o == null || getClass() != o.getClass()) return false;
+
+            final TableKey oKey = (TableKey) o;
+
+            if ( cycle != oKey.cycle ) return false;
+            if ( !readGroup.equals(oKey.readGroup) ) return false;
+
+            return true;
+        }
+
         @Override
         public int compareTo(final TableKey tableKey) {
             final int scmp = readGroup.compareTo(tableKey.readGroup);