fix test case paths
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3Driver.java
index bd08a78..28c4108 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3Driver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3Driver.java
@@ -42,8 +42,11 @@
@Option(name = "-kmer-size", usage = "the size of kmer", required = true)
public int sizeKmer;
- @Option(name = "-merge-rounds", usage = "the while rounds of merging", required = true)
+ @Option(name = "-merge-rounds", usage = "the maximum number of rounds to merge", required = false)
public int mergeRound;
+
+ @Option(name = "-hadoop-conf", usage = "an (optional) hadoop configuration xml", required = false)
+ public String hadoopConf;
}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
index 735c968..cc922de 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
@@ -22,10 +22,10 @@
protected String HDFS_MARKPATHS = "/02-pathmark/";
protected String HDFS_MERGED = "/03-pathmerge/";
- protected String GRAPHBUILD_FILE = "result.graphbuild.txt";
- protected String PATHMARKS_FILE = "result.markpaths.txt";
- protected String PATHMERGE_FILE = "result.mergepath.txt";
- protected boolean regenerateGraph = false;
+ protected String GRAPHBUILD_FILE = "graphbuild.result";
+ protected String PATHMARKS_FILE = "markpaths.result";
+ protected String PATHMERGE_FILE = "mergepath.result";
+ protected boolean regenerateGraph = true;
{
KMER_LENGTH = 5;
@@ -58,8 +58,7 @@
copyResultsToLocal(HDFS_MARKPATHS, ACTUAL_ROOT + PATHMARKS_FILE, false, conf);
MergePathsH3Driver h3 = new MergePathsH3Driver();
- h3.run(HDFS_MARKPATHS, HDFS_MERGED, 2, KMER_LENGTH, 10, null, conf);
-// h3.run(HDFS_MARKPATHS, HDFS_MERGED, 2, KMER_LENGTH, 10, HADOOP_CONF_ROOT + "conf.xml", null);
+ h3.run(HDFS_MARKPATHS, HDFS_MERGED, 2, KMER_LENGTH, 1, conf);
copyResultsToLocal(HDFS_MERGED, ACTUAL_ROOT + PATHMERGE_FILE, false, conf);
}