Complete NaiveBFSTraverse and make more test cases
diff --git a/genomix/genomix-pregelix/graph/BridgePath b/genomix/genomix-pregelix/graph/BridgePath
index c10ea60..fd735ea 100644
--- a/genomix/genomix-pregelix/graph/BridgePath
+++ b/genomix/genomix-pregelix/graph/BridgePath
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diff --git a/genomix/genomix-pregelix/graph/BridgePath_out.ps b/genomix/genomix-pregelix/graph/BridgePath_out.ps
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diff --git a/genomix/genomix-pregelix/graph/CyclePath b/genomix/genomix-pregelix/graph/CyclePath
index db30e3a..a487e90 100644
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diff --git a/genomix/genomix-pregelix/graph/mergeTest/BridgePath b/genomix/genomix-pregelix/graph/mergeTest/BridgePath
deleted file mode 100644
index 0717611..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/BridgePath
+++ /dev/null
@@ -1,2 +0,0 @@
-TTTCCACTCCGTG
-TTTCCACCCCGTG
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/graph/mergeTest/CyclePath b/genomix/genomix-pregelix/graph/mergeTest/CyclePath
deleted file mode 100644
index 04080f4..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/CyclePath
+++ /dev/null
@@ -1 +0,0 @@
-GCAACTTCATCAACT
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/graph/mergeTest/LongPath b/genomix/genomix-pregelix/graph/mergeTest/LongPath
deleted file mode 100644
index acd3c1a..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/LongPath
+++ /dev/null
@@ -1 +0,0 @@
-GGCCTCAGTACGCCCGG
diff --git a/genomix/genomix-pregelix/graph/mergeTest/Path b/genomix/genomix-pregelix/graph/mergeTest/Path
deleted file mode 100644
index f63bbcf..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/Path
+++ /dev/null
@@ -1 +0,0 @@
-GGCCTCAGTACG
diff --git a/genomix/genomix-pregelix/graph/mergeTest/SimplePath b/genomix/genomix-pregelix/graph/mergeTest/SimplePath
deleted file mode 100644
index 80c03af..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/SimplePath
+++ /dev/null
@@ -1,3 +0,0 @@
-ATATCGCATC
-AAGACAGCAC
-GCGGCAAGAA
diff --git a/genomix/genomix-pregelix/graph/mergeTest/SinglePath b/genomix/genomix-pregelix/graph/mergeTest/SinglePath
deleted file mode 100644
index 56ef5f8..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/SinglePath
+++ /dev/null
@@ -1 +0,0 @@
-AGACAACAGT
diff --git a/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer b/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer
deleted file mode 100644
index ec004fa..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/ThreeKmer
+++ /dev/null
@@ -1 +0,0 @@
-ACTCGGT
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TreePath b/genomix/genomix-pregelix/graph/mergeTest/TreePath
deleted file mode 100644
index f3c13ce..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/TreePath
+++ /dev/null
@@ -1,3 +0,0 @@
-GGCCTGGCTATCCC
-GGCCTCAGTAACTAAAC
-GGCCTCAGTACGCCCGG
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer b/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
deleted file mode 100644
index 8c2a74b..0000000
--- a/genomix/genomix-pregelix/graph/mergeTest/TwoKmer
+++ /dev/null
@@ -1 +0,0 @@
-ACACTG
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
index cd2425b..c686d0c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
@@ -32,6 +32,8 @@
private boolean updateMsg = false;
private VKmerBytesWritable startVertexId;
private VKmerListWritable pathList;
+ private boolean srcFlip = false;
+ private boolean destFlip = false;
private byte checkMessage;
@@ -264,6 +266,22 @@
}
}
+ public boolean isSrcFlip() {
+ return srcFlip;
+ }
+
+ public void setSrcFlip(boolean srcFlip) {
+ this.srcFlip = srcFlip;
+ }
+
+ public boolean isDestFlip() {
+ return destFlip;
+ }
+
+ public void setDestFlip(boolean destFlip) {
+ this.destFlip = destFlip;
+ }
+
@Override
public void write(DataOutput out) throws IOException {
out.writeInt(kmerlength);
@@ -284,6 +302,8 @@
out.writeBoolean(isFlip);
out.writeByte(flag);
out.writeBoolean(updateMsg);
+ out.writeBoolean(srcFlip);
+ out.writeBoolean(destFlip);
}
@Override
@@ -307,6 +327,8 @@
isFlip = in.readBoolean();
flag = in.readByte();
updateMsg = in.readBoolean();
+ srcFlip = in.readBoolean();
+ destFlip = in.readBoolean();
}
@Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
index f3abaed..ee42dee 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
@@ -6,11 +6,18 @@
import java.util.List;
import java.util.Map;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
public class BFSTraverseVertex extends
MapReduceVertex {
@@ -63,11 +70,11 @@
if (maxIteration < 0)
maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
if(incomingMsg == null)
- incomingMsg = new MessageWritable(kmerSize);
+ incomingMsg = new MessageWritable();
if(outgoingMsg == null)
- outgoingMsg = new MessageWritable(kmerSize);
+ outgoingMsg = new MessageWritable();
else
- outgoingMsg.reset(kmerSize);
+ outgoingMsg.reset();
if(reverseKmer == null)
reverseKmer = new VKmerBytesWritable();
if(kmerList == null)
@@ -82,6 +89,8 @@
if(destVertexId == null)
destVertexId = new VKmerBytesWritable(kmerSize);
isFakeVertex = ((byte)getVertexValue().getState() & State.FAKEFLAG_MASK) > 0 ? true : false;
+ if(tmpKmer == null)
+ tmpKmer = new VKmerBytesWritable();
}
public void aggregateMsgAndGroupedByReadIdInReachedNode(Iterator<MessageWritable> msgIterator){
@@ -124,6 +133,7 @@
}
public void initialBroadcaseBFSTraverse(){
+ outgoingMsg.reset();
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
outgoingMsg.getPathList().append(getVertexId());
@@ -135,6 +145,7 @@
}
public void broadcastBFSTraverse(){
+ outgoingMsg.reset();
outgoingMsg.setSourceVertexId(incomingMsg.getSourceVertexId());
outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
outgoingMsg.getPathList().append(getVertexId());
@@ -153,12 +164,19 @@
voteToHalt();
}
else if(getSuperstep() == 2){
- kmerList.append(new VKmerBytesWritable("Kmer1"));
- kmerList.append(new VKmerBytesWritable("Kmer2"));
+ tmpKmer.setByRead(kmerSize, "AAT".getBytes(), 0);
+ kmerList.append(tmpKmer);
+ tmpKmer.setByRead(kmerSize, "CTA".getBytes(), 0);
+ kmerList.append(tmpKmer);
/** initiate two nodes -- srcNode and destNode **/
srcNode.setAsCopy(kmerList.getPosition(0));
destNode.setAsCopy(kmerList.getPosition(1));
// outgoingMsg.setNodeIdList(); set as common readId
+ PositionWritable nodeId = new PositionWritable();
+ nodeId.set((byte) 0, 1, 0);
+ PositionListWritable nodeIdList = new PositionListWritable();
+ nodeIdList.append(nodeId);
+ outgoingMsg.setNodeIdList(nodeIdList);
outgoingMsg.setSeekedVertexId(destNode);
sendMsg(srcNode, outgoingMsg);
outgoingMsg.setSeekedVertexId(srcNode);
@@ -203,4 +221,17 @@
}
+ public static void main(String[] args) throws Exception {
+ PregelixJob job = new PregelixJob(BFSTraverseVertex.class.getSimpleName());
+ job.setVertexClass(BFSTraverseVertex.class);
+ /**
+ * BinaryInput and BinaryOutput
+ */
+ job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+ job.setDynamicVertexValueSize(true);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
+ job.setOutputValueClass(VertexValueWritable.class);
+ Client.run(args, job);
+ }
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/NaiveBFSTraverseVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/NaiveBFSTraverseVertex.java
new file mode 100644
index 0000000..d5b8301
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/NaiveBFSTraverseVertex.java
@@ -0,0 +1,189 @@
+package edu.uci.ics.genomix.pregelix.operator.scaffolding;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+
+public class NaiveBFSTraverseVertex extends
+ MapReduceVertex {
+
+ protected VKmerBytesWritable srcNode = new VKmerBytesWritable();
+ protected VKmerBytesWritable destNode = new VKmerBytesWritable();
+ Map<Long, List<MessageWritable>> receivedMsg = new HashMap<Long, List<MessageWritable>>();
+
+ /**
+ * initiate kmerSize, maxIteration
+ */
+ public void initVertex() {
+ if (kmerSize == -1)
+ kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+ if (maxIteration < 0)
+ maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+ if(incomingMsg == null)
+ incomingMsg = new MessageWritable();
+ if(outgoingMsg == null)
+ outgoingMsg = new MessageWritable();
+ else
+ outgoingMsg.reset();
+ if(reverseKmer == null)
+ reverseKmer = new VKmerBytesWritable();
+ if(kmerList == null)
+ kmerList = new VKmerListWritable();
+ else
+ kmerList.reset();
+ if(fakeVertex == null){
+ fakeVertex = new VKmerBytesWritable();
+ String random = generaterRandomString(kmerSize + 1);
+ fakeVertex.setByRead(kmerSize + 1, random.getBytes(), 0);
+ }
+ if(destVertexId == null)
+ destVertexId = new VKmerBytesWritable(kmerSize);
+ if(tmpKmer == null)
+ tmpKmer = new VKmerBytesWritable();
+ }
+
+ public void initialBroadcaseBFSTraverse(){
+ outgoingMsg.reset();
+ outgoingMsg.setSourceVertexId(getVertexId());
+ outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
+ outgoingMsg.setSrcFlip(incomingMsg.isSrcFlip());
+ outgoingMsg.setDestFlip(incomingMsg.isDestFlip());
+ kmerList.append(getVertexId());
+ outgoingMsg.setPathList(kmerList);
+ outgoingMsg.setNodeIdList(incomingMsg.getNodeIdList()); //only one readId
+ if(incomingMsg.isSrcFlip())
+ sendSettledMsgToAllPreviousNodes(getVertexValue());
+ else
+ sendSettledMsgToAllNextNodes(getVertexValue());
+ }
+
+ public void broadcaseBFSTraverse(){
+ outgoingMsg.reset();
+ outgoingMsg.setSourceVertexId(incomingMsg.getSourceVertexId());
+ outgoingMsg.setSeekedVertexId(incomingMsg.getSeekedVertexId());
+ outgoingMsg.setSrcFlip(incomingMsg.isSrcFlip());
+ outgoingMsg.setDestFlip(incomingMsg.isDestFlip());
+ kmerList.setCopy(incomingMsg.getPathList());
+ kmerList.append(getVertexId());
+ outgoingMsg.setPathList(kmerList);
+ outgoingMsg.setNodeIdList(incomingMsg.getNodeIdList()); //only one readId
+ byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+ byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ switch(neighborToMeDir){
+ case MessageFlag.DIR_FF:
+ case MessageFlag.DIR_FR:
+ sendSettledMsgToAllPreviousNodes(getVertexValue());
+ break;
+ case MessageFlag.DIR_RF:
+ case MessageFlag.DIR_RR:
+ sendSettledMsgToAllNextNodes(getVertexValue());
+ break;
+ }
+ }
+
+ public boolean isValidDestination(){
+ byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+ byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ if(incomingMsg.isDestFlip())
+ return neighborToMeDir == MessageFlag.DIR_RF || neighborToMeDir == MessageFlag.DIR_RR;
+ else
+ return neighborToMeDir == MessageFlag.DIR_FF || neighborToMeDir == MessageFlag.DIR_FR;
+ }
+
+ public void initiateSrcAndDestNode(VKmerListWritable pairKmerList, ArrayList<Boolean> flagList,
+ PositionListWritable nodeIdList){
+ initiateSrcAndDestNode(pairKmerList, flagList.get(0), flagList.get(1), nodeIdList);
+ }
+
+ public void initiateSrcAndDestNode(VKmerListWritable pairKmerList, boolean srcFlip, boolean destFlip,
+ PositionListWritable nodeIdList){
+ srcNode.setAsCopy(pairKmerList.getPosition(0));
+ destNode.setAsCopy(pairKmerList.getPosition(1));
+ outgoingMsg.setNodeIdList(nodeIdList);
+ outgoingMsg.setSeekedVertexId(destNode);
+ outgoingMsg.setSrcFlip(srcFlip);
+ outgoingMsg.setDestFlip(destFlip);
+ }
+
+ @Override
+ public void compute(Iterator<MessageWritable> msgIterator) {
+ initVertex();
+ if(getSuperstep() == 1){
+ addFakeVertex();
+ voteToHalt();
+ }
+ else if(getSuperstep() == 2){
+ tmpKmer.setByRead(kmerSize, "AAT".getBytes(), 0);
+ kmerList.append(tmpKmer);
+ tmpKmer.setByRead(kmerSize, "AGA".getBytes(), 0);
+ kmerList.append(tmpKmer);
+ // outgoingMsg.setNodeIdList(); set as common readId
+ PositionWritable nodeId = new PositionWritable();
+ nodeId.set((byte) 0, 1, 0);
+ PositionListWritable nodeIdList = new PositionListWritable();
+ nodeIdList.append(nodeId);
+ /** initiate two nodes -- srcNode and destNode **/
+ initiateSrcAndDestNode(kmerList, true, false, nodeIdList);
+ sendMsg(srcNode, outgoingMsg);
+
+ deleteVertex(getVertexId());
+ } else if(getSuperstep() == 3){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ /** begin to BFS **/
+ initialBroadcaseBFSTraverse();
+ }
+ voteToHalt();
+ } else if(getSuperstep() > 3){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ /** check if find destination **/
+ if(incomingMsg.getSeekedVertexId().equals(getVertexId())){
+ if(isValidDestination()){
+ kmerList.setCopy(incomingMsg.getPathList());
+ kmerList.append(getVertexId());
+ //TODO do some process after finding a path
+ }
+ else{
+ //keep BFS
+ broadcaseBFSTraverse();
+ }
+ } else {
+ //keep BFS
+ broadcaseBFSTraverse();
+ }
+ }
+ voteToHalt();
+ }
+
+ }
+
+ public static void main(String[] args) throws Exception {
+ PregelixJob job = new PregelixJob(NaiveBFSTraverseVertex.class.getSimpleName());
+ job.setVertexClass(NaiveBFSTraverseVertex.class);
+ /**
+ * BinaryInput and BinaryOutput
+ */
+ job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+ job.setDynamicVertexValueSize(true);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
+ job.setOutputValueClass(VertexValueWritable.class);
+ Client.run(args, job);
+ }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
index 782ed70..bf55cb1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
@@ -1,19 +1,60 @@
package edu.uci.ics.genomix.pregelix.operator.scaffolding;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import edu.uci.ics.genomix.pregelix.io.HashMapWritable;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
public class ScaffoldingVertex extends
- MapReduceVertex{
+ NaiveBFSTraverseVertex{
- public static Map<Long, VKmerListWritable> scaffoldingMap = new HashMap<Long, VKmerListWritable>();
+ public class KmerListAndFlagList{
+ private ArrayList<Boolean> flagList;
+ private VKmerListWritable kmerList;
+
+ public KmerListAndFlagList(){
+ flagList = new ArrayList<Boolean>();
+ kmerList = new VKmerListWritable();
+ }
+
+ public void set(KmerListAndFlagList kmerAndflag){
+ flagList.clear();
+ kmerList.reset();
+ flagList.addAll(kmerAndflag.getFlagList());
+ kmerList.appendList(kmerAndflag.getKmerList());
+ }
+
+ public int size(){
+ return flagList.size();
+ }
+
+ public ArrayList<Boolean> getFlagList() {
+ return flagList;
+ }
+
+ public void setFlagList(ArrayList<Boolean> flagList) {
+ this.flagList = flagList;
+ }
+
+ public VKmerListWritable getKmerList() {
+ return kmerList;
+ }
+
+ public void setKmerList(VKmerListWritable kmerList) {
+ this.kmerList = kmerList;
+ }
+
+ }
+ private ArrayList<Boolean> flagList = new ArrayList<Boolean>();
+ private KmerListAndFlagList kmerListAndflagList = new KmerListAndFlagList();
+ public static Map<Long, KmerListAndFlagList> scaffoldingMap = new HashMap<Long, KmerListAndFlagList>();
private HashMapWritable<VKmerBytesWritable, VKmerListWritable> traverseMap = new HashMapWritable<VKmerBytesWritable, VKmerListWritable>();
@@ -39,34 +80,74 @@
kmerList = new VKmerListWritable();
}
+ public void addStartReadsToScaffoldingMap(){
+ boolean isflip = false;
+ for(PositionWritable pos : getVertexValue().getStartReads()){
+ long readId = pos.getReadId();
+ if(scaffoldingMap.containsKey(readId)){
+ kmerList.setCopy(scaffoldingMap.get(readId).getKmerList());
+ kmerList.append(getVertexId());
+ flagList.clear();
+ flagList.addAll(scaffoldingMap.get(readId).getFlagList());
+ flagList.add(isflip);
+ } else{
+ kmerList.reset();
+ kmerList.append(getVertexId());
+ flagList.clear();
+ flagList.add(isflip);
+ }
+ kmerListAndflagList.setKmerList(kmerList);
+ kmerListAndflagList.setFlagList(flagList);
+ scaffoldingMap.put(readId, kmerListAndflagList);
+ }
+ }
+
+ public void addEndReadsToScaffoldingMap(){
+ boolean isflip = true;
+ for(PositionWritable pos : getVertexValue().getEndReads()){
+ long readId = pos.getReadId();
+ if(scaffoldingMap.containsKey(readId)){
+ kmerList.setCopy(scaffoldingMap.get(readId).getKmerList());
+ kmerList.append(getVertexId());
+ flagList.clear();
+ flagList.addAll(scaffoldingMap.get(readId).getFlagList());
+ flagList.add(isflip);
+ } else{
+ kmerList.reset();
+ kmerList.append(getVertexId());
+ flagList.clear();
+ flagList.add(isflip);
+ }
+ kmerListAndflagList.setKmerList(kmerList);
+ kmerListAndflagList.setFlagList(flagList);
+ scaffoldingMap.put(readId, kmerListAndflagList);
+ }
+ }
+
@Override
public void compute(Iterator<MessageWritable> msgIterator) {
initVertex();
if(getSuperstep() == 1){
/** add a fake vertex **/
addFakeVertex();
- /** grouped by 5' readId **/ //TODO
- long mainReadId = getVertexValue().getStartReads().getPosition(0).getReadId();
- if(mainReadId != 0){ //empty or not
- if(scaffoldingMap.containsKey(mainReadId)){
- kmerList.setCopy(scaffoldingMap.get(mainReadId));
- kmerList.append(getVertexId());
- } else{
- kmerList.reset();
- kmerList.append(getVertexId());
- }
- scaffoldingMap.put(mainReadId, kmerList);
- }
+ /** grouped by 5' readId **/
+ addStartReadsToScaffoldingMap();
+ addEndReadsToScaffoldingMap();
+
voteToHalt();
} else if(getSuperstep() == 2){
/** process scaffoldingMap **/
for(Long readId : scaffoldingMap.keySet()){
- kmerList.setCopy(scaffoldingMap.get(readId));
- if(kmerList.getCountOfPosition() == 2){
- outgoingMsg.setSeekedVertexId(kmerList.getPosition(1));
- sendMsg(kmerList.getPosition(0), outgoingMsg);
- outgoingMsg.setSeekedVertexId(kmerList.getPosition(0));
- sendMsg(kmerList.getPosition(1), outgoingMsg);
+ ////////////
+ PositionWritable nodeId = new PositionWritable();
+ nodeId.set((byte) 0, 1, 0);
+ PositionListWritable nodeIdList = new PositionListWritable();
+ nodeIdList.append(nodeId);
+ ////////////
+ kmerListAndflagList.set(scaffoldingMap.get(readId));
+ if(kmerListAndflagList.size() == 2){
+ initiateSrcAndDestNode(kmerListAndflagList.kmerList, kmerListAndflagList.flagList, nodeIdList);
+ sendMsg(srcNode, outgoingMsg);
}
}
deleteVertex(getVertexId());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SimpleSplitRepeatVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SimpleSplitRepeatVertex.java
new file mode 100644
index 0000000..3ab95b9
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SimpleSplitRepeatVertex.java
@@ -0,0 +1,29 @@
+package edu.uci.ics.genomix.pregelix.operator.splitrepeat;
+
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+public class SimpleSplitRepeatVertex extends
+ BasicGraphCleanVertex{
+
+ /**
+ * initiate kmerSize, maxIteration
+ */
+ public void initVertex() {
+ if (kmerSize == -1)
+ kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+ if (maxIteration < 0)
+ maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+ if(incomingMsg == null)
+ incomingMsg = new MessageWritable(kmerSize);
+ if(outgoingMsg == null)
+ outgoingMsg = new MessageWritable(kmerSize);
+ else
+ outgoingMsg.reset(kmerSize);
+ if(destVertexId == null)
+ destVertexId = new VKmerBytesWritable(kmerSize);
+ if(tmpKmer == null)
+ tmpKmer = new VKmerBytesWritable();
+ }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
index f30512c..f73a5de 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
@@ -9,24 +9,38 @@
/**
* Simple Path
*/
- public static String simplePath(int k, int length, int numLines) {
- RandomString rs = new RandomString(k, length);
+ public static String simplePath(int kmerSize, int readLength, int numLines) {
+ RandomString rs = new RandomString(kmerSize, readLength);
String output = "";
for (int i = 0; i < numLines; i++)
output += rs.nextString(0) + "\r\n";
return output;
+
}
/**
+ * Bridge Path
+ */
+ public static String bridgePath(int kmerSize, int headLength, int bridgeLength, int readLength) {
+ RandomString rs = new RandomString(kmerSize, readLength);
+ String s1 = rs.nextString(0);
+ rs.setLength(headLength + bridgeLength);
+ int startBridge = kmerSize + headLength;
+ rs.addString(s1.substring(0, startBridge));
+ String s2 = rs.nextString(startBridge) + s1.substring(bridgeLength + startBridge - kmerSize);
+ return s1 + "\r\n" + s2;
+ }
+
+ /**
* Tree Path
*/
- public static String treePath(int k, int x, int y, int z) {
- RandomString rs = new RandomString(k, x + y + k - 1);
+ public static String treePath(int kmerSize, int x, int y, int z) {
+ RandomString rs = new RandomString(kmerSize, x + y + kmerSize - 1);
String s1 = rs.nextString(0);
- rs.setLength(x + y + z + k - 1);
+ rs.setLength(x + y + z + kmerSize - 1);
rs.addString(s1.substring(0, x));
String s2 = rs.nextString(x);
- rs.setLength(x + y + z + k - 1);
+ rs.setLength(x + y + z + kmerSize - 1);
rs.addString(s2.substring(0, x + y));
String s3 = rs.nextString(x + y);
return s1 + "\r\n" + s2 + "\r\n" + s3;
@@ -35,46 +49,74 @@
/**
* Cycle Path
*/
- public static String cyclePath(int k, int length) {
- RandomString rs = new RandomString(k, length);
+ public static String cyclePath(int kmerSize, int length) {
+ RandomString rs = new RandomString(kmerSize, length);
String s1 = rs.nextString(0);
- String s2 = s1 + s1.substring(1, k + 1);
+ String s2 = s1 + s1.substring(1, kmerSize + 1);
return s2;
}
-
- /**
- * Bridge Path
- */
- public static String bridgePath(int k, int x) {
- RandomString rs = new RandomString(k, x + k + 2 + k - 1);
- String s1 = rs.nextString(0);
- rs.setLength(x + k + 2);
- rs.addString(s1.substring(0, k + 2));
- String s2 = rs.nextString(k + 2) + s1.substring(x + k + 2, x + k + 2 + k - 1);
- return s1 + "\r\n" + s2;
- }
-
- public static void main(String[] args) {
- // TODO Auto-generated method stub
+
+ public static void generateSimplePath(String destDir, int kmerSize, int readLength, int numLines){
OutputStreamWriter writer;
try {
- writer = new OutputStreamWriter(new FileOutputStream("graph/7/SinglePath"));
- writer.write(simplePath(7, 10, 1));
- writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/7/SimplePath"));
- writer.write(simplePath(7, 10, 3));
- writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/7/TreePath"));
- writer.write(treePath(7, 7, 7, 7));
- writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/7/CyclePath"));
- writer.write(cyclePath(7, 10));
- writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/7/BridgePath"));
- writer.write(bridgePath(7, 2));
+ writer = new OutputStreamWriter(new FileOutputStream(destDir));
+ writer.write(simplePath(kmerSize, readLength, numLines));
writer.close();
} catch (IOException e) {
e.printStackTrace();
}
}
+
+ public static void generateBridgePath(String destDir, int kmerSize, int headLength, int bridgeLength, int readLength){
+ OutputStreamWriter writer;
+ try {
+ writer = new OutputStreamWriter(new FileOutputStream(destDir));
+ writer.write(bridgePath(kmerSize, headLength, bridgeLength, readLength));
+ writer.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public static void generateTreePath(String destDir, int kmerSize, int x, int y, int z){
+ OutputStreamWriter writer;
+ try {
+ writer = new OutputStreamWriter(new FileOutputStream(destDir));
+ writer.write(treePath(kmerSize, x, y, z));
+ writer.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public static void generateCyclePath(String destDir, int kmerSize, int cycleLength){
+ OutputStreamWriter writer;
+ try {
+ writer = new OutputStreamWriter(new FileOutputStream(destDir));
+ writer.write(cyclePath(kmerSize, cycleLength));
+ writer.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public static void main(String[] args) {
+ int kmerSize = 3;
+ /** SimplePath **/
+ int readLength = 9;
+ int numLines = 3;
+ generateSimplePath("graph/SimplePath", kmerSize, readLength, numLines);
+ /** BridgePath **/
+ int headLength = 2;
+ int bridgeLength = 4;
+ generateBridgePath("graph/BridgePath", kmerSize, headLength, bridgeLength, readLength);
+ /** TreePath **/
+ int x = 5;
+ int y = 5;
+ int z = 5;
+ generateTreePath("graph/TreePath", kmerSize, x, y, z);
+ /** CyclePath **/
+ int cycleLength = 8;
+ generateCyclePath("graph/CyclePath", kmerSize, cycleLength);
+ }
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 98219d7..be6885b 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -17,6 +17,7 @@
import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.removelowcoverage.RemoveLowCoverageVertex;
+import edu.uci.ics.genomix.pregelix.operator.scaffolding.NaiveBFSTraverseVertex;
import edu.uci.ics.genomix.pregelix.operator.scaffolding.ScaffoldingVertex;
import edu.uci.ics.genomix.pregelix.operator.splitrepeat.SplitRepeatVertex;
import edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex;
@@ -249,6 +250,23 @@
+ "BubbleMergeGraph.xml");
}
+ private static void generateNaiveBFSTraverseGraphJob(String jobName, String outputPath) throws IOException {
+ PregelixJob job = new PregelixJob(jobName);
+ job.setVertexClass(NaiveBFSTraverseVertex.class);
+ job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+ job.setDynamicVertexValueSize(true);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
+ job.setOutputValueClass(VertexValueWritable.class);
+ job.getConfiguration().setInt(ScaffoldingVertex.KMER_SIZE, 3);
+ job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+ }
+
+ private static void genNaiveBFSTraverseGraph() throws IOException {
+ generateNaiveBFSTraverseGraphJob("NaiveBFSTraversegGraph", outputBase
+ + "NaiveBFSTraverseGraph.xml");
+ }
+
private static void generateScaffoldingGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
job.setVertexClass(ScaffoldingVertex.class);
@@ -278,6 +296,7 @@
genBubbleAddGraph();
genBubbleMergeGraph();
genSplitRepeatGraph();
+ genNaiveBFSTraverseGraph();
genScaffoldingGraph();
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BFSTraverseSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BFSTraverseSmallTestSuite.java
new file mode 100644
index 0000000..41b0d8b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BFSTraverseSmallTestSuite.java
@@ -0,0 +1,201 @@
+/*
+ * Copyright 2009-2010 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import junit.framework.Test;
+import junit.framework.TestResult;
+import junit.framework.TestSuite;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hdfs.MiniDFSCluster;
+import org.apache.hadoop.mapred.JobConf;
+
+import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
+import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
+
+@SuppressWarnings("deprecation")
+public class BFSTraverseSmallTestSuite extends TestSuite {
+ private static final Logger LOGGER = Logger.getLogger(BFSTraverseSmallTestSuite.class.getName());
+ //P4ForMergeGraph/bin/read
+ public static final String PreFix = "data/PathMergeTestSet";
+ public static final String[] TestDir = { PreFix + File.separator
+ + "4"};
+ private static final String ACTUAL_RESULT_DIR = "data/actual/BTSTraverse";
+ 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";
+ private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
+ private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
+ private static final String PATH_TO_ONLY = "src/test/resources/only_BFSTraverse.txt";
+
+ public static final String HDFS_INPUTPATH = "/PathTestSet";
+
+ private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+ private MiniDFSCluster dfsCluster;
+
+ private JobConf conf = new JobConf();
+ private int numberOfNC = 1;
+
+ public void setUp() throws Exception {
+ ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
+ ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
+ cleanupStores();
+ PregelixHyracksIntegrationUtil.init();
+ LOGGER.info("Hyracks mini-cluster started");
+ FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
+ FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
+ startHDFS();
+ }
+
+ private void startHDFS() throws IOException {
+ conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
+ conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
+ conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
+ FileSystem lfs = FileSystem.getLocal(new Configuration());
+ lfs.delete(new Path("build"), true);
+ System.setProperty("hadoop.log.dir", "logs");
+ dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
+ FileSystem dfs = FileSystem.get(conf);
+
+ for (String testDir : TestDir) {
+ File src = new File(testDir);
+ Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
+ dfs.mkdirs(dest);
+ //src.listFiles()
+ //src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
+ for (File f : src.listFiles()) {
+ dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
+ }
+ }
+
+ DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
+ conf.writeXml(confOutput);
+ confOutput.flush();
+ confOutput.close();
+ }
+
+ private void cleanupStores() throws IOException {
+ FileUtils.forceMkdir(new File("teststore"));
+ FileUtils.forceMkdir(new File("build"));
+ FileUtils.cleanDirectory(new File("teststore"));
+ FileUtils.cleanDirectory(new File("build"));
+ }
+
+ /**
+ * cleanup hdfs cluster
+ */
+ private void cleanupHDFS() throws Exception {
+ dfsCluster.shutdown();
+ }
+
+ public void tearDown() throws Exception {
+ PregelixHyracksIntegrationUtil.deinit();
+ LOGGER.info("Hyracks mini-cluster shut down");
+ cleanupHDFS();
+ }
+
+ public static Test suite() throws Exception {
+ List<String> onlys = getFileList(PATH_TO_ONLY);
+ File testData = new File(PATH_TO_JOBS);
+ File[] queries = testData.listFiles();
+ BFSTraverseSmallTestSuite testSuite = new BFSTraverseSmallTestSuite();
+ testSuite.setUp();
+ boolean onlyEnabled = false;
+ FileSystem dfs = FileSystem.get(testSuite.conf);
+
+ if (onlys.size() > 0) {
+ onlyEnabled = true;
+ }
+
+ for (File qFile : queries) {
+ if (qFile.isFile()) {
+ if (onlyEnabled && !isInList(onlys, qFile.getName())) {
+ continue;
+ } else {
+ for (String testPathStr : TestDir) {
+ File testDir = new File(testPathStr);
+ String resultFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "bin" + File.separator + testDir.getName();
+ String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
+ testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
+ .getAbsolutePath().toString(), dfs,
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
+ }
+ }
+ }
+ }
+ return testSuite;
+ }
+
+ /**
+ * Runs the tests and collects their result in a TestResult.
+ */
+ @Override
+ public void run(TestResult result) {
+ try {
+ int testCount = countTestCases();
+ for (int i = 0; i < testCount; i++) {
+ // cleanupStores();
+ Test each = this.testAt(i);
+ if (result.shouldStop())
+ break;
+ runTest(each, result);
+ }
+ tearDown();
+ } catch (Exception e) {
+ throw new IllegalStateException(e);
+ }
+ }
+
+ protected static List<String> getFileList(String ignorePath) throws FileNotFoundException, IOException {
+ BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
+ String s = null;
+ List<String> ignores = new ArrayList<String>();
+ while ((s = reader.readLine()) != null) {
+ ignores.add(s);
+ }
+ reader.close();
+ return ignores;
+ }
+
+ private static String jobExtToResExt(String fname) {
+ int dot = fname.lastIndexOf('.');
+ return fname.substring(0, dot);
+ }
+
+ private static boolean isInList(List<String> onlys, String name) {
+ for (String only : onlys)
+ if (name.indexOf(only) >= 0)
+ return true;
+ return false;
+ }
+
+}
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/NaiveBFSTraverseGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/NaiveBFSTraverseGraph.xml
new file mode 100644
index 0000000..a412b2b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/NaiveBFSTraverseGraph.xml
@@ -0,0 +1,142 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><configuration>
+<property><name>mapred.tasktracker.dns.nameserver</name><value>default</value></property>
+<property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
+<property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
+<property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
+<property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
+<property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
+<property><name>mapred.submit.replication</name><value>10</value></property>
+<property><name>ipc.server.tcpnodelay</name><value>false</value></property>
+<property><name>fs.checkpoint.dir</name><value>${hadoop.tmp.dir}/dfs/namesecondary</value></property>
+<property><name>mapred.output.compression.type</name><value>RECORD</value></property>
+<property><name>mapred.job.shuffle.merge.percent</name><value>0.66</value></property>
+<property><name>mapred.child.java.opts</name><value>-Xmx200m</value></property>
+<property><name>mapred.queue.default.acl-submit-job</name><value>*</value></property>
+<property><name>keep.failed.task.files</name><value>false</value></property>
+<property><name>mapred.jobtracker.job.history.block.size</name><value>3145728</value></property>
+<property><name>mapred.output.value.class</name><value>edu.uci.ics.genomix.pregelix.io.VertexValueWritable</value></property>
+<property><name>io.bytes.per.checksum</name><value>512</value></property>
+<property><name>mapred.task.tracker.report.address</name><value>127.0.0.1:0</value></property>
+<property><name>hadoop.util.hash.type</name><value>murmur</value></property>
+<property><name>fs.hdfs.impl</name><value>org.apache.hadoop.hdfs.DistributedFileSystem</value></property>
+<property><name>fs.ramfs.impl</name><value>org.apache.hadoop.fs.InMemoryFileSystem</value></property>
+<property><name>mapred.jobtracker.restart.recover</name><value>false</value></property>
+<property><name>fs.hftp.impl</name><value>org.apache.hadoop.hdfs.HftpFileSystem</value></property>
+<property><name>fs.checkpoint.period</name><value>3600</value></property>
+<property><name>mapred.child.tmp</name><value>./tmp</value></property>
+<property><name>mapred.local.dir.minspacekill</name><value>0</value></property>
+<property><name>map.sort.class</name><value>org.apache.hadoop.util.QuickSort</value></property>
+<property><name>hadoop.logfile.count</name><value>10</value></property>
+<property><name>ipc.client.connection.maxidletime</name><value>10000</value></property>
+<property><name>io.map.index.skip</name><value>0</value></property>
+<property><name>mapred.tasktracker.expiry.interval</name><value>600000</value></property>
+<property><name>mapred.output.compress</name><value>false</value></property>
+<property><name>io.seqfile.lazydecompress</name><value>true</value></property>
+<property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
+<property><name>fs.checkpoint.size</name><value>67108864</value></property>
+<property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
+<property><name>mapred.job.name</name><value>NaiveBFSTraversegGraph</value></property>
+<property><name>local.cache.size</name><value>10737418240</value></property>
+<property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
+<property><name>mapred.userlog.limit.kb</name><value>0</value></property>
+<property><name>fs.file.impl</name><value>org.apache.hadoop.fs.LocalFileSystem</value></property>
+<property><name>mapred.task.tracker.http.address</name><value>0.0.0.0:50060</value></property>
+<property><name>mapred.task.timeout</name><value>600000</value></property>
+<property><name>fs.kfs.impl</name><value>org.apache.hadoop.fs.kfs.KosmosFileSystem</value></property>
+<property><name>mapred.max.tracker.blacklists</name><value>4</value></property>
+<property><name>fs.s3.buffer.dir</name><value>${hadoop.tmp.dir}/s3</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.dir</name><value>/jobtracker/jobsInfo</value></property>
+<property><name>ipc.client.kill.max</name><value>10</value></property>
+<property><name>mapred.tasktracker.instrumentation</name><value>org.apache.hadoop.mapred.TaskTrackerMetricsInst</value></property>
+<property><name>mapred.reduce.tasks.speculative.execution</name><value>true</value></property>
+<property><name>io.sort.record.percent</name><value>0.05</value></property>
+<property><name>hadoop.security.authorization</name><value>false</value></property>
+<property><name>mapred.max.tracker.failures</name><value>4</value></property>
+<property><name>mapred.jobtracker.taskScheduler</name><value>org.apache.hadoop.mapred.JobQueueTaskScheduler</value></property>
+<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
+<property><name>mapred.map.tasks</name><value>2</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.hours</name><value>0</value></property>
+<property><name>fs.s3.sleepTimeSeconds</name><value>10</value></property>
+<property><name>fs.default.name</name><value>file:///</value></property>
+<property><name>mapred.output.key.class</name><value>edu.uci.ics.genomix.type.VKmerBytesWritable</value></property>
+<property><name>tasktracker.http.threads</name><value>40</value></property>
+<property><name>mapred.tasktracker.taskmemorymanager.monitoring-interval</name><value>5000</value></property>
+<property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
+<property><name>mapred.reduce.tasks</name><value>1</value></property>
+<property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
+<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.scaffolding.NaiveBFSTraverseVertex</value></property>
+<property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
+<property><name>io.file.buffer.size</name><value>4096</value></property>
+<property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
+<property><name>mapred.tasktracker.indexcache.mb</name><value>10</value></property>
+<property><name>mapred.tasktracker.map.tasks.maximum</name><value>2</value></property>
+<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
+<property><name>mapred.task.profile.maps</name><value>0-2</value></property>
+<property><name>hadoop.native.lib</name><value>true</value></property>
+<property><name>fs.s3.block.size</name><value>67108864</value></property>
+<property><name>mapred.job.reuse.jvm.num.tasks</name><value>1</value></property>
+<property><name>mapred.job.tracker.http.address</name><value>0.0.0.0:50030</value></property>
+<property><name>mapred.tasktracker.reduce.tasks.maximum</name><value>2</value></property>
+<property><name>io.compression.codecs</name><value>org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec</value></property>
+<property><name>mapred.job.shuffle.input.buffer.percent</name><value>0.70</value></property>
+<property><name>io.seqfile.compress.blocksize</name><value>1000000</value></property>
+<property><name>mapred.queue.names</name><value>default</value></property>
+<property><name>fs.har.impl</name><value>org.apache.hadoop.fs.HarFileSystem</value></property>
+<property><name>io.mapfile.bloom.error.rate</name><value>0.005</value></property>
+<property><name>mapred.job.tracker</name><value>local</value></property>
+<property><name>BasicGraphCleanVertex.kmerSize</name><value>3</value></property>
+<property><name>io.skip.checksum.errors</name><value>false</value></property>
+<property><name>mapred.reduce.max.attempts</name><value>4</value></property>
+<property><name>fs.s3.maxRetries</name><value>4</value></property>
+<property><name>ipc.server.listen.queue.size</name><value>128</value></property>
+<property><name>fs.trash.interval</name><value>0</value></property>
+<property><name>mapred.local.dir.minspacestart</name><value>0</value></property>
+<property><name>fs.s3.impl</name><value>org.apache.hadoop.fs.s3.S3FileSystem</value></property>
+<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
+<property><name>io.mapfile.bloom.size</name><value>1048576</value></property>
+<property><name>io.sort.mb</name><value>100</value></property>
+<property><name>mapred.local.dir</name><value>${hadoop.tmp.dir}/mapred/local</value></property>
+<property><name>io.sort.factor</name><value>10</value></property>
+<property><name>mapred.task.profile</name><value>false</value></property>
+<property><name>job.end.retry.interval</name><value>30000</value></property>
+<property><name>mapred.tasktracker.procfsbasedprocesstree.sleeptime-before-sigkill</name><value>5000</value></property>
+<property><name>mapred.jobtracker.completeuserjobs.maximum</name><value>100</value></property>
+<property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
+<property><name>webinterface.private.actions</name><value>false</value></property>
+<property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
+<property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
+<property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
+<property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
+<property><name>mapred.merge.recordsBeforeProgress</name><value>10000</value></property>
+<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
+<property><name>mapred.compress.map.output</name><value>false</value></property>
+<property><name>io.sort.spill.percent</name><value>0.80</value></property>
+<property><name>fs.checkpoint.edits.dir</name><value>${fs.checkpoint.dir}</value></property>
+<property><name>mapred.userlog.retain.hours</name><value>24</value></property>
+<property><name>mapred.system.dir</name><value>${hadoop.tmp.dir}/mapred/system</value></property>
+<property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
+<property><name>job.end.retry.attempts</name><value>0</value></property>
+<property><name>ipc.client.idlethreshold</name><value>4000</value></property>
+<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat</value></property>
+<property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
+<property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
+<property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
+<property><name>hadoop.logfile.size</name><value>10000000</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat</value></property>
+<property><name>mapred.job.queue.name</name><value>default</value></property>
+<property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
+<property><name>pregelix.incStateLength</name><value>true</value></property>
+<property><name>mapred.reduce.slowstart.completed.maps</name><value>0.05</value></property>
+<property><name>topology.script.number.args</name><value>100</value></property>
+<property><name>mapred.skip.map.max.skip.records</name><value>0</value></property>
+<property><name>fs.ftp.impl</name><value>org.apache.hadoop.fs.ftp.FTPFileSystem</value></property>
+<property><name>mapred.task.cache.levels</name><value>2</value></property>
+<property><name>mapred.job.tracker.handler.count</name><value>10</value></property>
+<property><name>io.serializations</name><value>org.apache.hadoop.io.serializer.WritableSerialization</value></property>
+<property><name>ipc.client.connect.max.retries</name><value>10</value></property>
+<property><name>mapred.min.split.size</name><value>0</value></property>
+<property><name>mapred.map.max.attempts</name><value>4</value></property>
+<property><name>jobclient.output.filter</name><value>FAILED</value></property>
+<property><name>ipc.client.tcpnodelay</name><value>false</value></property>
+<property><name>mapred.acls.enabled</name><value>false</value></property>
+</configuration>
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/test/resources/only_BFSTraverse.txt b/genomix/genomix-pregelix/src/test/resources/only_BFSTraverse.txt
new file mode 100644
index 0000000..92aae74
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/only_BFSTraverse.txt
@@ -0,0 +1 @@
+NaiveBFSTraverseGraph.xml