Merge branch 'jianfeng/genomix' into jianfeng/genomix-reverse
Conflicts:
genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeReadIDAggregateFactory.java
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index 11d0998..34fb0f6 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -132,6 +132,9 @@
public static int getCountByDataLength(int length) {
if (length % PositionWritable.LENGTH != 0) {
+ for (StackTraceElement ste : Thread.currentThread().getStackTrace()) {
+ System.out.println(ste);
+ }
throw new IllegalArgumentException("Length of positionlist is invalid");
}
return length / PositionWritable.LENGTH;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
index f614846..7ea065d 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
@@ -33,15 +33,15 @@
*
*/
private static final long serialVersionUID = 1L;
- private KmerBytesWritable kmer;
- private PositionListWritable plist;
-
+
+ private final int kmerSize;
public KMerTextWriterFactory(int k) {
- kmer = new KmerBytesWritable(k);
- plist = new PositionListWritable();
+ kmerSize =k;
}
public class TupleWriter implements ITupleWriter {
+ private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
+ private PositionListWritable plist = new PositionListWritable();
@Override
public void write(DataOutput output, ITupleReference tuple) throws HyracksDataException {
try {
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh
index c335475..5f89bcc 100644
--- a/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh
@@ -12,11 +12,11 @@
#Clean up temp dir
#rm -rf $NCTMP_DIR2
-mkdir $NCTMP_DIR2
+mkdir -p $NCTMP_DIR2
#Clean up log dir
#rm -rf $NCLOGS_DIR2
-mkdir $NCLOGS_DIR2
+mkdir -p $NCLOGS_DIR2
#Clean up I/O working dir
@@ -35,16 +35,14 @@
#Get node ID
NODEID=`hostname | cut -d '.' -f 1`
-NODEID=${NODEID}2
#Set JAVA_OPTS
export JAVA_OPTS=$NCJAVA_OPTS2
-cd $HYRACKS_HOME
-HYRACKS_HOME=`pwd`
+GENOMIX_HOME=`pwd`
#Enter the temp dir
cd $NCTMP_DIR2
#Launch hyracks nc
-$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
+${GENOMIX_HOME}/bin/genomixnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR -data-ip-address $IPADDR -result-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &