commit 94e075b5c3db9aa613ef61c2581430a143b17bc8
author Anbang Xu <anbangx@gmail.com> Mon Jul 29 11:08:40 2013 -0700
committer Anbang Xu <anbangx@gmail.com> Mon Jul 29 11:08:40 2013 -0700
tree ec21d0899cfa505c8811745651d840bb92bede27
parent 6ee7bdf0962e01af25f058d920800eb20e051406

update for merge

genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java

diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index 57d4a75..fbd458e 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -15,7 +15,9 @@
 
 package edu.uci.ics.genomix.data.test;
 
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import junit.framework.Assert;
@@ -386,5 +388,31 @@
         difference.addAll(s1);
         difference.removeAll(s2);
         System.out.println(difference.toString());
+        
+        Map<KmerBytesWritable, Set<Long>> map = new HashMap<KmerBytesWritable, Set<Long>>();
+        KmerBytesWritable k1 = new KmerBytesWritable(3);
+        Set<Long> set1 = new HashSet<Long>();
+        k1.setByRead(("CTA").getBytes(), 0);
+        set1.add((long)1);
+        map.put(k1, set1);
+        KmerBytesWritable k2 = new KmerBytesWritable(3);
+        k2.setByRead(("GTA").getBytes(), 0);
+        Set<Long> set2 = new HashSet<Long>();
+        set2.add((long) 2);
+        map.put(k2, set2);
+        KmerBytesWritable k3 = new KmerBytesWritable(3);
+        k3.setByRead(("ATG").getBytes(), 0);
+        Set<Long> set3 = new HashSet<Long>();
+        set3.add((long) 3);
+        map.put(k3, set3);
+        KmerBytesWritable k4 = new KmerBytesWritable(3);
+        k4.setByRead(("AAT").getBytes(), 0);
+        Set<Long> set4 = new HashSet<Long>();
+        set4.add((long) 4);
+        map.put(k4, set4);
+        System.out.println("CTA = " + map.get(k1).toString());
+        System.out.println("GTA = " + map.get(k2).toString());
+        System.out.println("ATG = " + map.get(k3).toString());
+        System.out.println("AAT = " + map.get(k4).toString());
     }
 }

genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java

diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
index 158104f..300d7b0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
@@ -206,8 +206,10 @@
                 }
                 for(KmerBytesWritable outgoingEdge : outgoingEdgeList){
                     for(KmerBytesWritable incomingEdge : incomingEdgeList){
-                        outgoingReadIdSet = kmerMap.get(outgoingEdge);
-                        incomingReadIdSet = kmerMap.get(incomingEdge);
+                        outgoingReadIdSet.clear();
+                        incomingReadIdSet.clear();
+                        outgoingReadIdSet.addAll(kmerMap.get(outgoingEdge));
+                        incomingReadIdSet.addAll(kmerMap.get(incomingEdge));
                         
                         //set all neighberEdge readId intersection
                         neighborEdgeIntersection.addAll(selfReadIdSet);