Example usage for org.apache.commons.cli Option getOpt

Introduction

In this page you can find the example usage for org.apache.commons.cli Option getOpt.

Prototype

public String getOpt() 

Source Link

Document

Retrieve the name of this Option.

Usage

From source file:tv.icntv.log.stb.core.AbstractJob.java

@Override
public int run(String[] args) throws Exception {
    if (null == args || args.length < 1) {
        logger.error("usage :-ruleFile <rule_file>");
        return -1;
    }/*from  www .j  a v  a 2 s. c o  m*/
    Map temp = Maps.newConcurrentMap();
    CommandLineParser parser = new PosixParser();
    CommandLine line = parser.parse(init(), args);

    for (Option option : line.getOptions()) {
        System.out.println(maps.get(option.getOpt()) + "\t" + option.getValue());
        temp.put(maps.get(option.getOpt()), option.getValue());
    }
    ;

    Configuration conf = super.getConf();

    conf.set("mapreduce.output.fileoutputformat.compress", "true");
    conf.set("mapreduce.output.fileoutputformat.compress.codec", "com.hadoop.compression.lzo.LzopCodec");
    conf.set("mapreduce.map.output.compress", "true");
    conf.set("mapreduce.map.output.compress.codec", "com.hadoop.compression.lzo.LzopCodec");
    return run(temp) ? 0 : 1;
}

---

From source file:uk.ac.ebi.mdk.apps.CommandLineMain.java

public void showHelp() {
    for (Object obj : toArray(new Option[0])) {
        Option opt = (Option) obj;
        System.out.println(String.format("    [%s|%s]\n        %s \n", opt.getOpt(), opt.getLongOpt(),
                opt.getDescription()));/*from  w  w  w  .  ja v  a 2s. co  m*/
    }
    System.exit(0);
}

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From source file:uni.bielefeld.cmg.sparkhit.hadoop.decodec.util.HelpParam.java

/**
 * print out help info with parameters/*w  ww.  j  av  a 2 s  .c  o  m*/
 */
public void printHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }
    });

    final String executable = System.getProperty("executable", "Hadoop jar sparkhit-hadoopDecompressor.jar");
    err.println("Name:");
    err.println("\tSparkHit hadoop decompressor");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tDeompressing BZip2 .bz2 file in parallel using Hadoop Mapper");
    err.println(executable + " [parameters] -bz2 hdfs://master/*/fastq.bz2 -outfile hdfs://master/out_dir");
    err.println(executable + " [parameters] -gz hdfs://master/*/fastq.gz -outfile hdfs://master/out_dir");
    err.println();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

/**
 * print out help info with parameters/*www.  j a v  a  2 s .  c o m*/
 */
public void printHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }
    });

    final String executable = System.getProperty("executable",
            "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.Main");
    err.println("Name:");
    err.println("\tSparkHit Main");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tBuild reference : ");
    err.println(executable + " [parameters] -build reference.fa");
    err.println("\trun fragment recruitment : ");
    err.println(executable + " [parameters] -fastq query.fq -reference reference.fa -outfile output_file.txt");
    err.println(executable + " [parameters] -line query.txt -reference reference.fa -outfile output_file.txt");
    err.println();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

public void printConverterHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }/*from w w  w  .j av  a  2 s  .  com*/
    });

    final String executable = System.getProperty("executable",
            "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfConverter Sparkhit.jar");
    err.println("Name:");
    err.println("\tSparkHit Converter");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tConvert different file format :");
    err.println(executable + " [parameters] -fastq query.fq.tar.bz2 -outfile ./outdir");
    err.println();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

public void printReporterHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }//from w w w.  ja v a2s.co m
    });

    final String executable = System.getProperty("executable",
            "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfReporter Sparkhit.jar");
    err.println("Name:");
    err.println("\tSparkHit Reporter");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tReport mappint summary");
    err.println(executable + " [parameters] -input ./sparkhit.out -outfile ./sparkhit.report");
    err.println();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

public void printScriptPiperHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }/*  w ww . j  a  va 2s .c o m*/
    });

    final String executable = System.getProperty("executable",
            "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfPiper Sparkhit.jar");
    err.println("Name:");
    err.println("\tSparkHit ScriptPiper (bwa, bowtie2 or other aligner)");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tParallelize your own tool like bwa mem:");
    err.println(executable
            + " [parameters] -fastq query.fq.tar.bz2 -outfile ./outbams_dir -tool \"/mypath/bwa mem\" -toolparam \"/mypath/reference.fa -t 32\"");
    err.println();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

public void printStatisticerHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }//from   w ww .  java 2  s .  c  o  m
    });

    final String executable = System.getProperty("executable",
            "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfPiper Sparkhit.jar");
    err.println("Name:");
    err.println("\tSparkHit Machine Learning library");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tMachine learning library for vcf or tabular file:");
    err.println(executable + " [parameters] -vcf genotype.vcf -outfile ./result -column 2-10 -cache");
    err.println();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

public void printDecompresserHelp() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new Comparator<Option>() {
        public int compare(Option o1, Option o2) {
            return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
        }//from   www . jav  a  2 s.co m
    });

    final String executable = System.getProperty("executable",
            "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfPiper Sparkhit.jar");
    err.println("Name:");
    err.println("\tSparkHit Decompresser");
    err.println();
    err.println("Options:");
    formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
    err.println();
    err.println("Usage:");
    err.println("\tDecomress zipball and tarball using spark codec:");
    err.println(executable + " [parameters] -fastq genotype.vcf -outfile ./decompressed");
    err.println();
}

---

From source file:vpp.Main.java

private VppOptions parseArgs() throws ParseException {
    final Option outputPathOption = new Option("o", "output-path", true,
            "The output file or directory. If not specified then the "
                    + "output is written to standard output.");

    final Option helpOption = new Option("h", "help", false, "Print help for this application and exit");

    final Options options = new Options();
    options.addOption(outputPathOption);
    options.addOption(helpOption);//  ww w.  jav a2  s.co m

    final GnuParser parser = new GnuParser();
    final CommandLine parsedArgs = parser.parse(options, this.args);
    final VppOptions vppOptions = new VppOptions();
    final String[] leftoverArgs = parsedArgs.getArgs();

    boolean printHelp = false;
    final Option[] parsedOptions = parsedArgs.getOptions();
    for (final Option option : parsedOptions) {
        final String value = option.getValue();
        if (option.getOpt().equals(helpOption.getOpt())) {
            printHelp = true;
        } else if (option.getOpt().equals(outputPathOption.getOpt())) {
            vppOptions.setDefine(value, "{post" + value + "}");
        }
    }

    for (final String leftoverArg : leftoverArgs) {
        vppOptions.addInputPath(leftoverArg);
    }

    if (printHelp) {
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("[options] [input paths]", options);
        return null;
    }

    return vppOptions;
}

---

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