public RunningJob run(String inputPath, String outputPath) throws Exception {
sLogger.info("Tool name: BuildGraph");
sLogger.info(" - input: " + inputPath);
sLogger.info(" - output: " + outputPath);
JobConf conf = new JobConf(BuildGraph.class);
conf.setJobName("BuildGraph " + inputPath + " " + ContrailConfig.K);
ContrailConfig.initializeConfiguration(conf);
FileInputFormat.addInputPath(conf, new Path(inputPath));
FileOutputFormat.setOutputPath(conf, new Path(outputPath));
conf.setInputFormat(TextInputFormat.class);
conf.setOutputFormat(TextOutputFormat.class);
conf.setMapOutputKeyClass(Text.class);
conf.setMapOutputValueClass(Text.class);
conf.setOutputKeyClass(Text.class);
conf.setOutputValueClass(Text.class);
conf.setMapperClass(BuildGraphMapper.class);
conf.setReducerClass(BuildGraphReducer.class);
// delete the output directory if it exists already
FileSystem.get(conf).delete(new Path(outputPath), true);
return JobClient.runJob(conf);
}
public int run(String[] args) throws Exception {
// TODO (jlewi): Currently the options specified here need to appear first on
// the command line otherwise we get an exeption when calling CommandLineParser.parse
// What we'd like to have happen is that any options not defined here
// get stored in CommandLine.args which get passed onto ContrailConfig.parseOptions.
Option kmer = new Option("k", "k", true, "k. The length of each kmer to use.");
Option input =
new Option(
"input",
"input",
true,
"The directory containing the input (i.e the output of BuildGraph.)");
Option output =
new Option(
"output", "output", true, "The directory where the output should be written to.");
Options options = new Options();
options.addOption(kmer);
options.addOption(input);
options.addOption(output);
CommandLineParser parser = new GnuParser();
CommandLine line = parser.parse(options, args, true);
if (!line.hasOption("input") || !line.hasOption("output") || !line.hasOption("k")) {
System.out.println("ERROR: Missing required arguments");
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("QuickMerge", options);
}
String inputPath = line.getOptionValue("input");
String outputPath = line.getOptionValue("output");
ContrailConfig.K = Integer.parseInt(line.getOptionValue("k"));
ContrailConfig.parseOptions(line.getArgs());
long starttime = System.currentTimeMillis();
run(inputPath, outputPath);
long endtime = System.currentTimeMillis();
float diff = (float) (((float) (endtime - starttime)) / 1000.0);
System.out.println("Runtime: " + diff + " s");
return 0;
}
