Example usage for org.apache.hadoop.mapred JobConf setMapOutputValueClass

List of usage examples for org.apache.hadoop.mapred JobConf setMapOutputValueClass

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Introduction

In this page you can find the example usage for org.apache.hadoop.mapred JobConf setMapOutputValueClass.

Prototype

public void setMapOutputValueClass(Class<?> theClass)

Source Link

Document

Set the value class for the map output data.

Usage

From source file:Corrector.Correction.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Correction [0/7]");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(Correction.class);
    conf.setJobName("Correction " + inputPath + " " + Config.K);

    Config.initializeConfiguration(conf);

    FileInputFormat.addInputPaths(conf, inputPath);
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);
    //conf.setBoolean("mapred.output.compress", true);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(CorrectionMapper.class);
    conf.setReducerClass(CorrectionReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.FindError.java

License:Apache License

public RunningJob run(String inputPath, String outputPath, int idx, String hkmerlist) throws Exception {
    sLogger.info("Tool name: FindError");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(FindError.class);
    conf.setJobName("FindError " + inputPath + " " + Config.K);
    conf.setLong("IDX", idx);
    //\\/*from w w  w.  j  a  va 2s  .c  om*/
    DistributedCache.addCacheFile(new URI(hkmerlist), conf);
    //\\

    Config.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(FindErrorMapper.class);
    conf.setReducerClass(FindErrorReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.Graph2Fasta.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Graph2Fasta [7/7]");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(Graph2Fasta.class);
    conf.setJobName("Graph2Fasta " + inputPath);

    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(Graph2FastaMapper.class);

    Config.initializeConfiguration(conf);
    conf.setNumReduceTasks(0);/* w w  w  .  j  ava  2  s.c  o m*/

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.Graph2Sfa.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Graph2Sfa [0/7]");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(Graph2Sfa.class);
    conf.setJobName("Graph2Sfa " + inputPath);

    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(Graph2SfaMapper.class);

    Config.initializeConfiguration(conf);
    conf.setNumReduceTasks(0);/*  w  w w. ja  v a  2s .  com*/

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.IdentifyTrustedReads.java

License:Apache License

public RunningJob run(String inputPath, String outputPath, long kmer_threshold) throws Exception {
    sLogger.info("Tool name: IdentifyTrustedReads");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(IdentifyTrustedReads.class);
    conf.setJobName("IdentifyTrustedReads " + inputPath + " " + Config.K);
    conf.setLong("KmerThreshold", kmer_threshold);
    // conf.setLong("AllKmer", allkmer);

    Config.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(IntWritable.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(IntWritable.class);

    conf.setMapperClass(IdentifyTrustedReads.IdentifyTrustedReadsMapper.class);
    conf.setReducerClass(IdentifyTrustedReads.IdentifyTrustedReadsReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.KmerFrequencyOfReads.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: KmerFrequencyOfReads");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(KmerFrequencyOfReads.class);
    conf.setJobName("KmerFrequencyOfReads " + inputPath + " " + Config.K);

    Config.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(IntWritable.class);
    conf.setMapOutputValueClass(Text.class);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(KmerFrequencyOfReads.KmerFrequencyOfReadsMapper.class);
    conf.setReducerClass(KmerFrequencyOfReads.KmerFrequencyOfReadsReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.PCorrection.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: PCorrection");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(PCorrection.class);
    conf.setJobName("PCorrection " + inputPath + " " + Config.K);

    Config.initializeConfiguration(conf);

    FileInputFormat.addInputPaths(conf, inputPath);
    FileOutputFormat.setOutputPath(conf, new Path(outputPath));

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    conf.setMapOutputKeyClass(Text.class);
    conf.setMapOutputValueClass(Text.class);
    //conf.setBoolean("mapred.output.compress", true);

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(PCorrectionMapper.class);
    conf.setReducerClass(PCorrectionReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.PreCorrect.java

License:Apache License

public RunningJob run(String inputPath, String outputPath, int idx, String hkmerlist) throws Exception {
    sLogger.info("Tool name: PreCorrect");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(PreCorrect.class);
    conf.setJobName("PreCorrect " + inputPath + " " + Config.K);
    conf.setLong("IDX", idx);
    //\\// w  w  w .  j a v a2 s  .  c o m
    DistributedCache.addCacheFile(new URI(hkmerlist), conf);
    //\\

    Config.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(PreCorrectMapper.class);
    conf.setReducerClass(PreCorrectReducer.class);

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:Corrector.PreProcessReads.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: PreProcessReads");
    sLogger.info(" - input: " + inputPath);
    sLogger.info(" - output: " + outputPath);

    JobConf conf = new JobConf(PreProcessReads.class);
    conf.setJobName("PreProcessReads " + inputPath + " " + Config.K);

    Config.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(PreProcessReadsMapper.class);
    //conf.setReducerClass(PreProcessReadsReducer.class);
    conf.setNumReduceTasks(0);//from w ww. j  av  a2 s . c o  m

    //delete the output directory if it exists already
    FileSystem.get(conf).delete(new Path(outputPath), true);

    return JobClient.runJob(conf);
}

From source file:crunch.MaxTemperature.java

License:Apache License

@Override
    public int run(String[] args) throws IOException {
        JobConf conf = JobBuilder.parseInputAndOutput(this, getConf(), args);
        if (conf == null) {
            return -1;
        }/*from   w  w w  . j av a2  s  .  c o m*/

        /*[*/conf.setInputFormat(TextInputFormat.class);

        conf.setNumMapTasks(1);
        conf.setMapperClass(IdentityMapper.class);
        conf.setMapRunnerClass(MapRunner.class);

        conf.setMapOutputKeyClass(LongWritable.class);
        conf.setMapOutputValueClass(Text.class);

        conf.setPartitionerClass(HashPartitioner.class);

        conf.setNumReduceTasks(1);
        conf.setReducerClass(IdentityReducer.class);

        conf.setOutputKeyClass(LongWritable.class);
        conf.setOutputValueClass(Text.class);

        conf.setOutputFormat(TextOutputFormat.class);/*]*/

        JobClient.runJob(conf);
        return 0;
    }