modify the test parameter
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
index 329d3f6..841f9f8 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
@@ -79,6 +79,7 @@
private KmerListWritable edgeListForPreKmer = new KmerListWritable();
private KmerListWritable edgeListForNextKmer = new KmerListWritable();
private NodeWritable outputNode = new NodeWritable();
+ private NodeWritable outputNode2 = new NodeWritable();
private KmerBytesWritable preForwardKmer = new KmerBytesWritable();
private KmerBytesWritable preReverseKmer = new KmerBytesWritable();
@@ -147,12 +148,64 @@
}
/*last kmer*/
- outputNode.reset();
+/* outputNode.reset();
setPreKmerByOldCurKmer();
setCurKmerByOldNextKmer();
setnodeId(mateId, readID, 0);//array.length - kmerSize + 1
setEdgeListForPreKmer();
- writeToFrame(writer);
+ writeToFrame(writer);*/
+ preKmerDir = curKmerDir;
+ preForwardKmer.setAsCopy(curForwardKmer);
+ preReverseKmer.setAsCopy(curReverseKmer);
+
+ curKmerDir = nextKmerDir;
+ curForwardKmer.setAsCopy(nextForwardKmer);
+ curReverseKmer.setAsCopy(nextReverseKmer);
+
+ nodeId.set(mateId, readID, 0);
+ nodeIdList.reset();
+ nodeIdList.append(nodeId);
+ outputNode2.setNodeIdList(nodeIdList);
+
+ switch(curKmerDir){
+ case FORWARD:
+ switch(preKmerDir){
+ case FORWARD:
+ edgeListForPreKmer.reset();
+ edgeListForPreKmer.append(preForwardKmer);
+ outputNode2.setRRList(edgeListForPreKmer);
+ break;
+ case REVERSE:
+ edgeListForPreKmer.reset();
+ edgeListForPreKmer.append(preReverseKmer);
+ outputNode2.setRFList(edgeListForPreKmer);
+ break;
+ }
+ break;
+ case REVERSE:
+ switch(preKmerDir){
+ case FORWARD:
+ edgeListForPreKmer.reset();
+ edgeListForPreKmer.append(preForwardKmer);
+ outputNode2.setFRList(edgeListForPreKmer);
+ break;
+ case REVERSE:
+ edgeListForPreKmer.reset();
+ edgeListForPreKmer.append(preReverseKmer);
+ outputNode2.setFFList(edgeListForPreKmer);
+ break;
+ }
+ break;
+ }
+
+ switch(curKmerDir){
+ case FORWARD:
+ InsertToFrame(curForwardKmer, outputNode2, writer);
+ break;
+ case REVERSE:
+ InsertToFrame(curReverseKmer, outputNode2, writer);
+ break;
+ }
}
public void setnodeId(byte mateId, long readID, int posId){
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
index 5409f34..4602ed2 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/driver/Driver.java
@@ -120,9 +120,7 @@
private void execute(JobSpecification job) throws Exception {
job.setUseConnectorPolicyForScheduling(false);
- if(profiling)
- EnumSet.of(JobFlag.PROFILE_RUNTIME);
- JobId jobId = hcc.startJob(job, EnumSet.of(JobFlag.PROFILE_RUNTIME));
+ JobId jobId = hcc.startJob(job, profiling ? EnumSet.of(JobFlag.PROFILE_RUNTIME) : EnumSet.noneOf(JobFlag.class));
hcc.waitForCompletion(jobId);
}
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
index 3cd5bb9..25915aa 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
@@ -32,7 +32,7 @@
@SuppressWarnings("deprecation")
public class JobRun {
private static final int KmerSize = 5;
- private static final int ReadLength = 8;
+ private static final int ReadLength = 6;
private static final String ACTUAL_RESULT_DIR = "actual";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
diff --git a/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt b/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt
index 17770fa..3f1cd5c 100644
--- a/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt
+++ b/genomix/genomix-hyracks/src/test/resources/data/webmap/test1.txt
@@ -1 +1 @@
-1 AATAGAAG
+1 AATAGA