new h2
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 1f790eb..614c696 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
@@ -183,11 +183,7 @@
int pos = ((kmerlength - 1) % 4) << 1;
byte code = (byte) (c << pos);
bytes[0] = (byte) (((bytes[0] >>> 2) & 0x3f) | code);
-<<<<<<< HEAD
- return (byte) output;
-=======
return output;
->>>>>>> 230f23a445dc7904a45bc535ebd73c3f4c619081
}
/**
@@ -215,16 +211,13 @@
byte in = (byte) ((bytes[i + 1] >> 6) & 0x03);
bytes[i] = (byte) ((bytes[i] << 2) | in);
}
+ bytes[size - 1] = (byte) ((bytes[size - 1] << 2) | c);
// (k%4) * 2
if (kmerlength % 4 != 0) {
bytes[0] &= (1 << ((kmerlength % 4) << 1)) - 1;
}
- bytes[size - 1] = (byte) ((bytes[size - 1] << 2) | c);
-<<<<<<< HEAD
- return (byte) output;
-=======
+
return output;
->>>>>>> 230f23a445dc7904a45bc535ebd73c3f4c619081
}
public void set(KmerBytesWritable newData) {
diff --git a/genomix/genomix-hadoop/actual3/complete2/.complete2-r-00000.crc b/genomix/genomix-hadoop/actual3/complete2/.complete2-r-00000.crc
new file mode 100644
index 0000000..bccc1b3
--- /dev/null
+++ b/genomix/genomix-hadoop/actual3/complete2/.complete2-r-00000.crc
Binary files differ
diff --git a/genomix/genomix-hadoop/actual3/complete2/complete2-r-00000 b/genomix/genomix-hadoop/actual3/complete2/complete2-r-00000
new file mode 100755
index 0000000..2704be9
--- /dev/null
+++ b/genomix/genomix-hadoop/actual3/complete2/complete2-r-00000
Binary files differ
diff --git a/genomix/genomix-hadoop/actual3/conf.xml b/genomix/genomix-hadoop/actual3/conf.xml
index 9c045a4..3434825 100644
--- a/genomix/genomix-hadoop/actual3/conf.xml
+++ b/genomix/genomix-hadoop/actual3/conf.xml
@@ -12,7 +12,11 @@
<property><name>dfs.namenode.logging.level</name><value>info</value></property>
<property><name>dfs.datanode.address</name><value>127.0.0.1:0</value></property>
<property><name>io.skip.checksum.errors</name><value>false</value></property>
+<<<<<<< Updated upstream
<property><name>fs.default.name</name><value>hdfs://localhost:55383</value></property>
+=======
+<property><name>fs.default.name</name><value>hdfs://localhost:50310</value></property>
+>>>>>>> Stashed changes
<property><name>mapred.child.tmp</name><value>./tmp</value></property>
<property><name>fs.har.impl.disable.cache</name><value>true</value></property>
<property><name>dfs.safemode.threshold.pct</name><value>0.999f</value></property>
@@ -125,7 +129,11 @@
<property><name>mapred.map.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
<property><name>mapred.tasktracker.dns.interface</name><value>default</value></property>
<property><name>dfs.namenode.decommission.interval</name><value>3</value></property>
+<<<<<<< Updated upstream
<property><name>dfs.http.address</name><value>localhost:55384</value></property>
+=======
+<property><name>dfs.http.address</name><value>localhost:50311</value></property>
+>>>>>>> Stashed changes
<property><name>dfs.heartbeat.interval</name><value>3</value></property>
<property><name>mapred.job.tracker</name><value>local</value></property>
<property><name>io.seqfile.sorter.recordlimit</name><value>1000000</value></property>
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store
index 92eedd1..8f46380 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store
new file mode 100644
index 0000000..f5eb144
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/gbresultschecking/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store
new file mode 100644
index 0000000..f9e3926
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
index f7a3457..fb55e18 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathMapper.java
@@ -33,6 +33,7 @@
private VKmerBytesWritable tmpKmer;
private VKmerBytesWritable outputKmer;
+
public void configure(JobConf job) {
KMER_SIZE = job.getInt("sizeKmer", 0);
outputKmerFactory = new VKmerBytesWritableFactory(KMER_SIZE);
@@ -52,8 +53,7 @@
precursor = (byte) (precursor & adjBitMap);
precursor = (byte) ((precursor & 0xff) >> 4);
succeed = (byte) (succeed & adjBitMap);
-
- if (bitFlag == 1) {
+ if (bitFlag == 1) {
byte succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
index 513b02c..921b233 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathReducer.java
@@ -34,7 +34,6 @@
private int KMER_SIZE;
private MergePathValueWritable outputValue;
private MergePathValueWritable tmpOutputValue;
-
MultipleOutputs mos = null;
private int I_MERGE;
@@ -106,13 +105,14 @@
mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
}
}
- }
+ }
} else {
if (outputValue.getFlag() != 0) {
tmpKmer.set(kmerFactory.getFirstKmerFromChain(KMER_SIZE-1, key));
outputKmer.set(kmerFactory.mergeTwoKmer(outputValue.getKmer(), tmpKmer));
outputValue.set(null, 0, 0, outputValue.getAdjBitMap(), outputValue.getFlag(), 0);
mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
+
} else
mos.getCollector("uncomplete" + I_MERGE, reporter).collect(key, outputValue);
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
index a6e6c92..5f04565 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/MergePathValueWritable.java
@@ -94,7 +94,7 @@
}
public String toString() {
- return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag) + '\t' + kmer.toString();
+ return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag);
}
@Override
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
index 0bfe86d..617ecf0 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialMapper.java
@@ -97,7 +97,6 @@
@Override
public void map(KmerBytesWritable key, ByteWritable value,
OutputCollector<KmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
-
byte precursor = (byte) 0xF0;
byte succeed = (byte) 0x0F;
byte adjBitMap = value.get();
@@ -107,7 +106,6 @@
succeed = (byte) (succeed & adjBitMap);
boolean inDegree = measureDegree(precursor);
boolean outDegree = measureDegree(succeed);
-
if (inDegree == false && outDegree == false) {
outputKmer.set(key);
bitFlag = (byte) 2;
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
index 89daa6c..2723b47 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmerging/SNodeInitialReducer.java
@@ -29,6 +29,7 @@
private VKmerBytesWritable outputKmer = new VKmerBytesWritable();
private MergePathValueWritable outputValue = new MergePathValueWritable();
+
@Override
public void reduce(KmerBytesWritable key, Iterator<MergePathValueWritable> values,
OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
new file mode 100644
index 0000000..b955fcd
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/ENodeInitialReducer.java
@@ -0,0 +1,59 @@
+package edu.uci.ics.pathmergingh2;
+
+import java.io.IOException;
+import java.util.Iterator;
+import org.apache.hadoop.io.BytesWritable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import edu.uci.ics.genomix.type.KmerUtil;
+
+@SuppressWarnings("deprecation")
+public class ENodeInitialReducer extends MapReduceBase implements
+ Reducer<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
+ public BytesWritable outputKmer = new BytesWritable();
+ public MergePathValueWritable outputAdjList = new MergePathValueWritable();
+
+
+ @Override
+ public void reduce(BytesWritable key, Iterator<MergePathValueWritable> values,
+ OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
+ outputAdjList = values.next();
+ outputKmer.set(key);
+ if (values.hasNext() == true) {
+ byte bitFlag = outputAdjList.getFlag();
+ bitFlag = (byte) (bitFlag & 0xFE);
+ if (bitFlag == 2) {
+ bitFlag = (byte) (0x80 | outputAdjList.getFlag());
+ outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerLength());
+ output.collect(outputKmer, outputAdjList);
+
+ } else {
+ boolean flag = false;
+ while (values.hasNext()) {
+ outputAdjList = values.next();
+ if (outputAdjList.getFlag() == 2) {
+ flag = true;
+ break;
+ }
+ }
+ if (flag == true) {
+ bitFlag = (byte) (0x80 | outputAdjList.getFlag());
+ outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerLength());
+ output.collect(outputKmer, outputAdjList);
+ }
+ }
+ } else {
+ byte bitFlag = outputAdjList.getFlag();
+ bitFlag = (byte) (bitFlag & 0xFE);
+ if (bitFlag == 2) {
+ bitFlag = 0;
+ outputAdjList.set(null, 0, 0, outputAdjList.getAdjBitMap(), bitFlag, outputAdjList.getKmerLength());
+ output.collect(outputKmer, outputAdjList);
+ }
+ }
+ }
+}
+
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
index 7a18eb7..ca7f259 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Driver.java
@@ -55,7 +55,7 @@
conf.setJobName("Initial Path-Starting-Points Table");
conf.setMapperClass(SNodeInitialMapper.class);
conf.setReducerClass(SNodeInitialReducer.class);
-
+
conf.setMapOutputKeyClass(KmerBytesWritable.class);
conf.setMapOutputValueClass(MergePathValueWritable.class);
@@ -88,14 +88,9 @@
conf.setReducerClass(MergePathReducer.class);
conf.setMapOutputKeyClass(VKmerBytesWritable.class);
- conf.setMapOutputValueClass(MergePathValueWritable.class);
-
- conf.setInputFormat(SequenceFileInputFormat.class);
-
- String uncomplete = "uncomplete" + iMerge;
- String complete = "complete" + iMerge;
-
- MultipleOutputs.addNamedOutput(conf, uncomplete,
+ conf.setMapOutputKeyClass(BytesWritable.class);
+
+<<<<<<< Updated upstream
MergePathMultiSeqOutputFormat.class, VKmerBytesWritable.class,
MergePathValueWritable.class);
@@ -114,6 +109,7 @@
dfs.delete(new Path(inputPath + "-step1"), true);
dfs.rename(new Path(outputPath + "/" + uncomplete), new Path(inputPath + "-step1"));
dfs.rename(new Path(outputPath + "/" + complete), new Path(mergeResultPath + "/" + complete));
+<<<<<<< Updated upstream
}
conf = new JobConf(MergePathDriver.class);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
index 69106df..3c5b192 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Mapper.java
@@ -16,7 +16,7 @@
private int KMER_SIZE;
private VKmerBytesWritableFactory outputKmerFactory;
- private MergePathValueWritable outputValue;
+ private MergePathValueWritable outputValue;
private VKmerBytesWritable tmpKmer;
private VKmerBytesWritable outputKmer;
@@ -27,6 +27,7 @@
tmpKmer = new VKmerBytesWritable(KMER_SIZE);
outputKmer = new VKmerBytesWritable(KMER_SIZE);
}
+
@Override
public void map(VKmerBytesWritable key, MergePathValueWritable value,
OutputCollector<VKmerBytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
@@ -36,15 +37,15 @@
byte bitFlag = value.getFlag();
precursor = (byte) (precursor & adjBitMap);
precursor = (byte) ((precursor & 0xff) >> 4);
- succeed = (byte) (succeed & adjBitMap);
+ succeed = (byte) (succeed & adjBitMap);
byte bitStartEnd = (byte) (0x81 & bitFlag);
-
+
switch (bitStartEnd) {
case 0x01:
byte succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
-
+
tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
bitFlag = (byte) (bitFlag | 0x08);
outputValue.set(tmpKmer, adjBitMap, bitFlag);
@@ -62,12 +63,12 @@
succeedCode = GeneCode.getGeneCodeFromBitMap(succeed);
tmpKmer.set(outputKmerFactory.getLastKmerFromChain(KMER_SIZE, key));
outputKmer.set(outputKmerFactory.shiftKmerWithNextCode(tmpKmer, succeedCode));
-
+
tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(key.getKmerLength() - (KMER_SIZE - 1), key));
bitFlag = (byte) (bitFlag | 0x08);
outputValue.set(tmpKmer, adjBitMap, bitFlag);
output.collect(outputKmer, outputValue);
-
+
bitFlag = (byte) (bitFlag & 0xF7);
tmpKmer.set(outputKmerFactory.getFirstKmerFromChain(KMER_SIZE, key));
outputKmer.set(tmpKmer);//?????
@@ -78,7 +79,7 @@
break;
case (byte) 0x81:
outputKmer.set(key);
- outputValue.set(null, 0, 0, adjBitMap, bitFlag, 0);//????????
+ outputValue.set(null, 0, 0, adjBitMap, bitFlag, 0);//????????
break;
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
index d206926..5d5b872 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathH2Reducer.java
@@ -2,6 +2,7 @@
import java.io.IOException;
import java.util.Iterator;
+
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.OutputCollector;
@@ -25,6 +26,7 @@
MultipleOutputs mos = null;
private int I_MERGE;
+
public void configure(JobConf job) {
mos = new MultipleOutputs(job);
I_MERGE = Integer.parseInt(job.get("iMerge"));
@@ -92,6 +94,7 @@
outputKmer.set(key);
mos.getCollector("complete" + I_MERGE, reporter).collect(outputKmer, outputValue);
}
+
}
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
index c3fbe1c..5a6b722 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/MergePathValueWritable.java
@@ -43,9 +43,10 @@
kmer.set(bytes, 0, bytes.length);
}
- public void set (MergePathValueWritable right) {
+ public void set(MergePathValueWritable right) {
set(right.getBytes(), 0, right.getLength(), right.getAdjBitMap(), right.getFlag(), right.getKmerLength());
}
+
public void set(KmerBytesWritable mergedKmer, byte adjBitMap, byte bitFlag) {
set(mergedKmer.getBytes(), 0, mergedKmer.getLength(), adjBitMap, bitFlag, mergedKmer.getKmerLength());
}
@@ -69,6 +70,7 @@
@Override
public void write(DataOutput arg0) throws IOException {
// TODO Auto-generated method stub
+
kmer.write(arg0);
arg0.writeByte(adjBitMap);
arg0.writeByte(flag);
@@ -105,6 +107,7 @@
public int getKmerLength() {
return kmer.getKmerLength();
}
+
@Override
public int getLength() {
return kmer.getLength();
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
index 75ac0d1..498b7c8 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialMapper.java
@@ -95,9 +95,14 @@
int a = 2;
int b = a;
}
+ if (key.toString().equals("TCG")) {
+ int a = 2;
+ int b = a;
+ }
if (inDegree == false && outDegree == false) {
outputKmer.set(key);
+ System.out.println(outputKmer.hashCode());
bitFlag = (byte) 2;
outputAdjList.set(null, 0, 0, adjBitMap, bitFlag, 0);
output.collect(outputKmer, outputAdjList);
@@ -111,8 +116,11 @@
byte precurCode = GeneCode.getGeneCodeFromBitMap(temp);
shiftedCode = key.shiftKmerWithPreCode(precurCode);
outputKmer.set(key);
+ for(int j = 0; j < key.getLength(); j ++){
+ System.out.println(key.getBytes()[j]);
+ }
bitFlag = (byte) 0x80;
- outputAdjList.set(null, 0, 0, (byte) 6, bitFlag, 0);
+ outputAdjList.set(null, 0, 0, (byte) 0, bitFlag, 0);
output.collect(outputKmer, outputAdjList);
key.shiftKmerWithNextCode(shiftedCode);
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
index 3d2b58c..e840965 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/pathmergingh2/SNodeInitialReducer.java
@@ -35,10 +35,10 @@
startFlag = 0x01;
break;
case (byte) 0x80:
- endFlag = 0x01;
+ endFlag = (byte) 0x80;
break;
case (byte) 0x02:
- targetPointFlag = 0x01;
+ targetPointFlag = 0x02;
targetAdjList = outputValue.getAdjBitMap();
break;
}
@@ -46,13 +46,13 @@
outputValue = values.next();
switch (outputValue.getFlag()) {
case (byte) 0x01:
- startFlag = 0x01;
+ startFlag = (byte) 0x01;
break;
case (byte) 0x80:
- endFlag = 0x01;
+ endFlag = (byte) 0x80;
break;
case (byte) 0x02:
- targetPointFlag = 0x02;
+ targetPointFlag = (byte) 0x02;
targetAdjList = outputValue.getAdjBitMap();
break;
}
@@ -60,10 +60,10 @@
break;
}
if(targetPointFlag == 0x02) {
- if(startFlag == 0x01) {
+ if(startFlag == (byte) 0x01) {
outputFlag = (byte) (outputFlag | startFlag);
}
- if(endFlag == 0x80) {
+ if(endFlag == (byte) 0x80) {
outputFlag = (byte) (outputFlag | endFlag);
}
outputValue.set(null, 0, 0, targetAdjList, outputFlag, 0);
diff --git a/genomix/genomix-hadoop/src/test/.DS_Store b/genomix/genomix-hadoop/src/test/.DS_Store
new file mode 100644
index 0000000..bfe14e8
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/.DS_Store b/genomix/genomix-hadoop/src/test/java/.DS_Store
new file mode 100644
index 0000000..fb3684c
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/.DS_Store b/genomix/genomix-hadoop/src/test/java/edu/.DS_Store
new file mode 100644
index 0000000..f50e64b
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/.DS_Store b/genomix/genomix-hadoop/src/test/java/edu/uci/.DS_Store
new file mode 100644
index 0000000..9aea623
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/.DS_Store b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/.DS_Store
new file mode 100644
index 0000000..64f18c4
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/.DS_Store
Binary files differ
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
index 285e554..01b3884 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/pathmergingh2/MergePathH2Test.java
@@ -16,7 +16,6 @@
import org.apache.hadoop.mapred.MiniMRCluster;
import org.apache.hadoop.util.ReflectionUtils;
import org.junit.Test;
-
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.utils.TestUtils;
@@ -103,5 +102,4 @@
Path dest = new Path(ACTUAL_RESULT_DIR + "/");
dfs.copyToLocalFile(src, dest);
}
-}
-
+}
\ No newline at end of file