Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
index 3d93baa..9befdbb 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
@@ -485,16 +485,7 @@
FileSystem dfs = FileSystem.get(conf);
conf.setJarByClass(MergePathsH4.class);
conf.setJobName("MergePathsH4 " + inputPath);
-<<<<<<< HEAD
-
- //another comment
- FileInputFormat.addInputPaths(conf, inputPath);
- Path outputPath = new Path(inputPath + ".h4merge.tmp");
- FileOutputFormat.setOutputPath(conf, outputPath);
-
-=======
->>>>>>> 0fd527e9535a755b9d0956adb1cdc845f1fc46c2
conf.setInputFormat(SequenceFileInputFormat.class);
conf.setOutputFormat(SequenceFileOutputFormat.class);
conf.setMapOutputKeyClass(PositionWritable.class);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
index 2765920..98fe5f6 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4Driver.java
@@ -112,28 +112,6 @@
break;
}
}
-<<<<<<< HEAD
-
- // finally, combine all the completed paths and update messages to
- // create a single merged graph output
- dfs.delete(new Path(outputGraphPath), true); // clear any previous
- // output
- // use all the "complete" and "update" outputs in addition to the final
- // (possibly empty) toMerge directories
- // as input to the final update step. This builds a comma-delim'ed
- // String of said files.
- final String lastMergeOutput = mergeOutput;
- PathFilter updateFilter = new PathFilter() {
- @Override
- public boolean accept(Path arg0) {
- String path = arg0.toString();
- System.out.println("equals last: " + path + " vs " + lastMergeOutput + " = " + path.endsWith(lastMergeOutput));
- return (path.matches(".*" + COMPLETE + "_i\\d+$") || path.matches(".*" + UPDATES + "_i\\d+$") || path.endsWith(lastMergeOutput));
- }
- };
- // test comment
-
-=======
if (!mergeComplete) {
// if the merge didn't finish, we have to do one final iteration to convert back into (NodeWritable, NullWritable) pairs
ConvertGraphFromNodeWithFlagToNodeWritable converter = new ConvertGraphFromNodeWithFlagToNodeWritable();
@@ -142,7 +120,6 @@
}
// final output string is a comma-separated list of completeOutputs
->>>>>>> 0fd527e9535a755b9d0956adb1cdc845f1fc46c2
StringBuilder sb = new StringBuilder();
String delim = "";
for (String output : completeOutputs) {