add global variable
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
index abdc8fd..66e0f43 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
@@ -7,8 +7,9 @@
import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
public class VertexUtil {
- private static VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(
+ public static VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(
NaiveAlgorithmForPathMergeVertex.kmerSize);
+ public static VKmerBytesWritable subKmer = new VKmerBytesWritable(0);
/**
* Single Vertex: in-degree = out-degree = 1
* @param vertexValue
@@ -55,8 +56,7 @@
* check if mergeChain is cycle
*/
public static boolean isCycle(KmerBytesWritable vertexId, VKmerBytesWritable mergeChain, int kmerSize){
- VKmerBytesWritable subKmer;
- for(int istart = 1; istart < mergeChain.getKmerLength() - kmerSize; istart++) {
+ for(int istart = 1; istart < mergeChain.getKmerLength() - kmerSize + 1; istart++) {
subKmer = kmerFactory.getSubKmerFromChain(istart, kmerSize, mergeChain);
if(subKmer.equals(vertexId))
return true;