| commit | aac7732cc3e118d9a99fdb5d70d2dae421ecf015 | [log] [tgz] |
|---|---|---|
| author | Anbang Xu <anbangx@gmail.com> | Tue Jul 30 22:22:26 2013 -0700 |
| committer | Anbang Xu <anbangx@gmail.com> | Tue Jul 30 22:22:26 2013 -0700 |
| tree | 10c00803bcc556f40639597080190d6a33fcaf9d | |
| parent | 34d3d7352da17956a3850489f305497a33a2e13b [diff] |
SimpleSplitRepeat is completed. An issue in graph building(hadoop): KmerList.appendList() doesn't check existed element
diff --git a/genomix/genomix-hadoop/data/webmap/AdjSplitRepeat.txt b/genomix/genomix-hadoop/data/webmap/AdjSplitRepeat.txt new file mode 100644 index 0000000..f2e3942 --- /dev/null +++ b/genomix/genomix-hadoop/data/webmap/AdjSplitRepeat.txt
@@ -0,0 +1,3 @@ +1 AATAG +2 GCATA +3 ATAGC
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java index 1633c26..687474b 100644 --- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java +++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -36,7 +36,7 @@ while (values.hasNext()) { tmpNode.set(values.next()); outputNode.getNodeIdList().appendList(tmpNode.getNodeIdList()); - outputNode.getFFList().appendList(tmpNode.getFFList()); + outputNode.getFFList().appendList(tmpNode.getFFList()); //appendList need to check if insert node exists outputNode.getFRList().appendList(tmpNode.getFRList()); outputNode.getRFList().appendList(tmpNode.getRFList()); outputNode.getRRList().appendList(tmpNode.getRRList());
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java index 127ab3e..ca7f67d 100644 --- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java +++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTest.java
@@ -22,7 +22,7 @@ private JobConf conf = new JobConf(); private static final String ACTUAL_RESULT_DIR = "actual"; private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml"; - private static final String DATA_PATH = "data/webmap/SplitRepeat.txt"; + private static final String DATA_PATH = "data/webmap/AdjSplitRepeat.txt"; private static final String HDFS_PATH = "/webmap"; private static final String RESULT_PATH = "/result";