fix mergeWithRFKmer
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 96e1cc4..da6dd0d 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -467,7 +467,8 @@
posnInByte = 0;
}
}
- bytes[offset] = cacheByte;
+ if(cacheByte != 0)
+ bytes[offset] = cacheByte;
clearLeadBit();
}
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 b4361ac..bda73e5 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
@@ -236,7 +236,7 @@
k1.setByRead(test1.getBytes(), 0);
k2.setByRead(test2.getBytes(), 0);
k1.mergeWithRFKmer(3, k2);
- Assert.assertEquals("CTAT", k1);
+ Assert.assertEquals("TCTA", k1.toString());
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 7185616..49bca8e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -6,12 +6,13 @@
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.genomix.oldtype.PositionWritable;
import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.type.MessageFromHead;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
/*
* vertexId: BytesWritable
* vertexValue: VertexValueWritable
@@ -44,7 +45,7 @@
BasicPathMergeVertex {
private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
- PositionWritable tempPostition = new PositionWritable();
+ KmerBytesWritable tempPostition = new KmerBytesWritable();
/**
* initiate kmerSize, maxIteration
@@ -207,8 +208,8 @@
/**
* BinaryInput and BinaryOutput~/
*/
- job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class);
- job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
+ job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setOutputKeyClass(PositionWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.setDynamicVertexValueSize(true);
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 5aedeb7..115f090 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -45,14 +45,14 @@
public static final String PreFix = "data/PathMergeTestSet"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
-// + "2", PreFix + File.separator
-// + "3", PreFix + File.separator
-// + "4", PreFix + File.separator
-// + "5", PreFix + File.separator
-// + "6", PreFix + File.separator
-// + "7", PreFix + File.separator
-// + "8", PreFix + File.separator
- + "4"};
+ + "2", PreFix + File.separator
+ + "3", PreFix + File.separator
+ + "4", PreFix + File.separator
+ + "5", PreFix + File.separator
+ + "6", PreFix + File.separator
+ + "7", PreFix + File.separator
+ + "8", PreFix + File.separator
+ + "9"};
private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";