facilitate better testing via more constructors and proper hashing/equals
diff --git a/genomix/genomix-hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
index 610092a..8ca2fa3 100755
--- a/genomix/genomix-hadoop/pom.xml
+++ b/genomix/genomix-hadoop/pom.xml
@@ -174,5 +174,11 @@
<type>test-jar</type>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.apache.mrunit</groupId>
+ <artifactId>mrunit</artifactId>
+ <version>1.0.0</version>
+ <classifier>hadoop1</classifier>
+ </dependency>
</dependencies>
</project>
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 eaf2a6f..c735a0d 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
@@ -52,6 +52,7 @@
public void run(String inputPath, String outputPath, int numReducers, int sizeKmer, int readLength,
boolean onlyTest1stJob, boolean seqOutput, String defaultConfPath) throws IOException {
if (onlyTest1stJob == true) {
+
runfirstjob(inputPath, numReducers, sizeKmer, readLength, seqOutput, defaultConfPath);
} else {
runfirstjob(inputPath, numReducers, sizeKmer, readLength, true, defaultConfPath);
@@ -113,6 +114,7 @@
conf.setPartitionerClass(ReadIDPartitioner.class);
+ // grouping is done on the readID only; sorting is based on the (readID, abs(posn))
conf.setOutputKeyComparatorClass(PositionWritable.Comparator.class);
conf.setOutputValueGroupingComparator(PositionWritable.FirstComparator.class);