add reversed kmer option
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@3301 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
index 3e80ab7..f9bf5b0 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
@@ -45,6 +45,7 @@
+ HDFS_OUTPUT_PATH + "/merged.txt";
private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
private static final String EXPECTED_PATH = "src/test/resources/expected/result2";
+ private static final String EXPECTED_REVERSE_PATH = "src/test/resources/expected/result_reverse";
private static final String HYRACKS_APP_NAME = "genomix";
private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
@@ -125,33 +126,59 @@
TestPreClusterGroupby();
cleanUpReEntry();
TestHybridGroupby();
+ cleanUpReEntry();
+ conf.setBoolean(GenomixJob.REVERSED_KMER, true);
+ TestExternalReversedGroupby();
+ cleanUpReEntry();
+ TestPreClusterReversedGroupby();
+ cleanUpReEntry();
+ TestHybridReversedGroupby();
}
public void TestExternalGroupby() throws Exception {
conf.set(GenomixJob.GROUPBY_TYPE, "external");
- conf.set(GenomixJob.OUTPUT_FORMAT, "binary");
System.err.println("Testing ExternalGroupBy");
driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
- Assert.assertEquals(true, checkResults());
+ Assert.assertEquals(true, checkResults(EXPECTED_PATH));
}
public void TestPreClusterGroupby() throws Exception {
conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
- conf.set(GenomixJob.OUTPUT_FORMAT, "binary");
System.err.println("Testing PreClusterGroupBy");
driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
- Assert.assertEquals(true, checkResults());
+ Assert.assertEquals(true, checkResults(EXPECTED_PATH));
}
public void TestHybridGroupby() throws Exception {
conf.set(GenomixJob.GROUPBY_TYPE, "hybrid");
- conf.set(GenomixJob.OUTPUT_FORMAT, "binary");
System.err.println("Testing HybridGroupBy");
driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
- Assert.assertEquals(true, checkResults());
+ Assert.assertEquals(true, checkResults(EXPECTED_PATH));
+ }
+
+ public void TestExternalReversedGroupby() throws Exception{
+ conf.set(GenomixJob.GROUPBY_TYPE, "external");
+ conf.setBoolean(GenomixJob.REVERSED_KMER, true);
+ System.err.println("Testing ExternalGroupBy + Reversed");
+ driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+ Assert.assertEquals(true, checkResults(EXPECTED_REVERSE_PATH));
+ }
+ public void TestPreClusterReversedGroupby() throws Exception{
+ conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
+ conf.setBoolean(GenomixJob.REVERSED_KMER, true);
+ System.err.println("Testing PreclusterGroupBy + Reversed");
+ driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+ Assert.assertEquals(true, checkResults(EXPECTED_REVERSE_PATH));
+ }
+ public void TestHybridReversedGroupby() throws Exception{
+ conf.set(GenomixJob.GROUPBY_TYPE, "hybrid");
+ conf.setBoolean(GenomixJob.REVERSED_KMER, true);
+ System.err.println("Testing HybridGroupBy + Reversed");
+ driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+ Assert.assertEquals(true, checkResults(EXPECTED_REVERSE_PATH));
}
- private boolean checkResults() throws Exception {
+ private boolean checkResults(String expectedPath) throws Exception {
File dumped = null;
String format = conf.get(GenomixJob.OUTPUT_FORMAT);
if ("text".equalsIgnoreCase(format)) {
@@ -206,7 +233,7 @@
dumped = new File(CONVERT_RESULT);
}
- TestUtils.compareWithSortedResult(new File(EXPECTED_PATH), dumped);
+ TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
return true;
}
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_reverse b/genomix/genomix-hyracks/src/test/resources/expected/result_reverse
new file mode 100644
index 0000000..cf2712d
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/expected/result_reverse
@@ -0,0 +1,8 @@
+AAGAT G|A 5
+AATAG |A 5
+AGAAG T| 5
+AGATA A|A 5
+ATAGA A|A 5
+GAAGA |T 5
+GATAA A| 5
+TAGAA A|G 5