modify building
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java
index 7f9e995..ccbabd7 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/DeepGraphBuildingMapper.java
@@ -32,10 +32,15 @@
@Override
public void map(KmerBytesWritable key, PositionListWritable value, OutputCollector<PositionWritable, PositionListAndKmerWritable> output,
Reporter reporter) throws IOException {
+ if(key.toString().equals("AGAAG")) {
+ int y = 4;
+ int x = y;
+ }
listPosZeroInRead.reset();
listPosNonZeroInRead.reset();
outputListAndKmer.reset();
- for(int i = 0; i < value.getLength(); i++) {
+ System.out.println(value.getLength());
+ for(int i = 0; i < value.getCountOfPosition(); i++) {
VertexID.set(value.getPosition(i));
if(VertexID.getPosInRead() == 0) {
listPosZeroInRead.append(VertexID);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java
index 3bd1bf8..4726380 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/GraphBuildingDriver.java
@@ -82,7 +82,8 @@
FileInputFormat.setInputPaths(conf, new Path(inputPath));
FileOutputFormat.setOutputPath(conf, new Path(inputPath + "-step1"));
- conf.setNumReduceTasks(numReducers);
+ if(numReducers == 0)
+ conf.setNumReduceTasks(numReducers + 2);
FileSystem dfs = FileSystem.get(conf);
dfs.delete(new Path(inputPath + "-step1"), true);
@@ -100,26 +101,24 @@
conf.setMapperClass(DeepGraphBuildingMapper.class);
conf.setReducerClass(DeepGraphBuildingReducer.class);
-
conf.setMapOutputKeyClass(PositionWritable.class);
conf.setMapOutputValueClass(PositionListAndKmerWritable.class);
-
conf.setPartitionerClass(ReadIDPartitioner.class);
- conf.setOutputKeyComparatorClass(PositionWritable.Comparator.class);
- conf.setOutputValueGroupingComparator(PositionWritable.FirstComparator.class);
+ // conf.setOutputKeyComparatorClass(PositionWritable.Comparator.class);
+ // conf.setOutputValueGroupingComparator(PositionWritable.FirstComparator.class);
conf.setInputFormat(SequenceFileInputFormat.class);
if (seqOutput == true)
conf.setOutputFormat(SequenceFileOutputFormat.class);
else
conf.setOutputFormat(TextOutputFormat.class);
- if(numReducers != 0){
- conf.setOutputKeyClass(NodeWritable.class);
- conf.setOutputValueClass(NullWritable.class);
- }
- else {
+
+ if (numReducers != 0) {
+ conf.setOutputKeyClass(NodeWritable.class);
+ conf.setOutputValueClass(NullWritable.class);
+ } else {
conf.setOutputKeyClass(PositionWritable.class);
conf.setOutputValueClass(PositionListAndKmerWritable.class);
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
index fff3faf..9becd58 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
@@ -60,6 +60,7 @@
this.vertexIDList.set(list);
this.kmer.set(kmer);
}
+
@Override
public void readFields(DataInput in) throws IOException {
this.countOfKmer = in.readInt();
@@ -78,4 +79,8 @@
public int compareTo(PositionListAndKmerWritable o) {
return 0;
}
+
+ public String toString() {
+ return vertexIDList.toString() + "\t" + kmer.toString();
+ }
}