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

Introduction

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

Prototype

public void setInputFormat(Class<? extends InputFormat> theClass) 

Source Link

Document

Set the InputFormat implementation for the map-reduce job.

Usage

From source file:Brush.GenNonContainedReads.java

License:Apache License

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

    JobConf conf = new JobConf(Stats.class);
    conf.setJobName("GenNonContainedReads " + inputPath + " " + BrushConfig.K);

    BrushConfig.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.setBoolean("mapred.output.compress", true);
    //conf.setClass("mapred.output.compression.codec", GzipCodec.class,CompressionCodec.class);

    conf.setMapperClass(GenNonContainedReadsMapper.class);
    conf.setReducerClass(GenNonContainedReadsReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.GenReverseEdge.java

License:Apache License

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

    //JobConf conf = new JobConf(Stats.class);
    JobConf conf = new JobConf(GenReverseEdge.class);
    conf.setJobName("GenReverseEdge " + inputPath);

    BrushConfig.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.setBoolean("mapred.output.compress", true);

    conf.setMapperClass(GenReverseEdgeMapper.class);
    conf.setReducerClass(GenReverseEdgeReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.Graph2Fasta.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Graph2Fasta");
    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);

    BrushConfig.initializeConfiguration(conf);
    conf.setNumReduceTasks(0);/*from   w  w  w . ja v a 2s.  c  o  m*/

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

    return JobClient.runJob(conf);
}

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From source file:Brush.Graph2Sfa.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) throws Exception {
    sLogger.info("Tool name: Graph2Sfa");
    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);

    BrushConfig.initializeConfiguration(conf);
    conf.setNumReduceTasks(0);/* w  w w .  j  a v a  2  s .c  om*/

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

    return JobClient.runJob(conf);
}

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From source file:Brush.KmerStatus.java

License:Apache License

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

    JobConf conf = new JobConf(KmerStatus.class);
    conf.setJobName("KmerStatus " + inputPath + " " + BrushConfig.K);
    // conf.setLong("AllKmer", allkmer);

    BrushConfig.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.setBoolean("mapred.output.compress", true);

    conf.setMapperClass(KmerStatusMapper.class);
    conf.setReducerClass(KmerStatusReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.MatchPrefix.java

License:Apache License

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

    JobConf conf = new JobConf(MatchPrefix.class);
    conf.setJobName("MatchPrefix " + inputPath + " " + BrushConfig.K);
    conf.setLong("AllKmer", allkmer);
    conf.setLong("DiffKmer", diffkmer);
    conf.setLong("AllReads", nodes);

    BrushConfig.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(MatchPrefixMapper.class);
    conf.setReducerClass(MatchPrefixReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.PairMark.java

License:Apache License

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

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

    BrushConfig.initializeConfiguration(conf);
    conf.setLong("randseed", randseed);

    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(PairMarkMapper.class);
    conf.setReducerClass(PairMarkReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.PairMerge.java

License:Apache License

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

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

    BrushConfig.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(PairMergeMapper.class);
    conf.setReducerClass(PairMergeReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.PopBubbles.java

License:Apache License

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

    JobConf conf = new JobConf(PopBubbles.class);
    conf.setJobName("PopBubbles " + inputPath + " " + BrushConfig.K);

    BrushConfig.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.setBoolean("mapred.output.compress", true);

    conf.setMapperClass(PopBubblesMapper.class);
    conf.setReducerClass(PopBubblesReducer.class);

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

    return JobClient.runJob(conf);
}

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From source file:Brush.PreCorrect.java

License:Apache License

public RunningJob run(String inputPath, String outputPath) 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 + " " + BrushConfig.K);

    BrushConfig.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);
}

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