Example usage for org.apache.commons.cli PosixParser parse

Introduction

In this page you can find the example usage for org.apache.commons.cli PosixParser parse.

Prototype

public CommandLine parse(Options options, String[] arguments, Properties properties) throws ParseException 

Source Link

Document

Parse the arguments according to the specified options and properties.

Usage

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();//www .j  a  v  a2 s.c o  m

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(IDENTITY)) != null) {
            if (Integer.decode(value) >= 0 || Integer.decode(value) <= 100) {
                param.readIdentity = Integer.decode(value);
                if (param.readIdentity >= 94) {
                    param.setKmerOverlap(0);
                    param.setKmerSize(12);
                }
            } else {
                throw new RuntimeException("Parameter " + IDENTITY + " should not be integer of %");
            }
        }

        if ((value = cl.getOptionValue(KMER_SIZE)) != null) {
            if (Integer.decode(value) >= 8 || Integer.decode(value) <= 12) {
                param.kmerSize = Integer.decode(value);
                param.setKmerSize(param.kmerSize);
            } else {
                throw new RuntimeException("Parameter " + KMER_SIZE + " should be set between 8-12");
            }
        }

        if ((value = cl.getOptionValue(OVERLAP)) != null) {
            if (Integer.decode(value) >= 0 || Integer.decode(value) <= param.kmerSize) {
                param.kmerOverlap = Integer.decode(value);
            } else {
                throw new RuntimeException(
                        "Parameter " + OVERLAP + " should not be bigger than kmer size or smaller than 0");
            }
        }

        /**
         * not available for now
         */
        if ((value = cl.getOptionValue(BUILD_REF)) != null) {
            param.inputBuildPath = new File(value).getAbsolutePath();
            param.inputFaPath = param.inputBuildPath;
            return param;
        }

        if ((value = cl.getOptionValue(THREADS)) != null) {
            if (Integer.decode(value) <= threads) {
                param.threads = Integer.decode(value);
            } else if (Integer.decode(value) == 0) {
                param.threads = threads;
            } else if (Integer.decode(value) < 0) {
                throw new RuntimeException(
                        "Parameter " + THREADS + " come on, CPU number could not be smaller than 1");
            } else {
                throw new RuntimeException("Parameter " + THREADS
                        + " is bigger than the number of your CPUs. Should be smaller than " + threads);
            }
        }

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(EVALUE)) != null) {
            param.eValue = Double.parseDouble(value);
        }

        if ((value = cl.getOptionValue(GLOBAL)) != null) {
            param.globalOrLocal = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(UNMASK)) != null) {
            if (Integer.decode(value) == 1 || Integer.decode(value) == 0) {
                param.maskRepeat = Integer.decode(value);
            } else {
                throw new RuntimeException("Parameter " + UNMASK + " should be set as 1 or 0");
            }
        }

        if ((value = cl.getOptionValue(COVERAGE)) != null) {
            param.alignLength = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(MINLENGTH)) != null) {
            if (Integer.decode(value) >= 0) {
                param.minReadSize = Integer.decode(value);
            } else {
                throw new RuntimeException("Parameter " + MINLENGTH + " should be larger than 0");
            }
        }

        if ((value = cl.getOptionValue(ATTEMPTS)) != null) {
            if (Integer.decode(value) >= 1) {
                param.maxTrys = Integer.decode(value);
            } else {
                throw new RuntimeException("Parameter " + ATTEMPTS + " at least try once");
            }
        }

        if ((value = cl.getOptionValue(HITS)) != null) {
            if (Integer.decode(value) >= 0) {
                param.reportRepeatHits = Integer.decode(value);
            } else {
                throw new RuntimeException("Parameter " + HITS + " should be bigger than 0");
            }
        }

        if ((value = cl.getOptionValue(STRAND)) != null) {
            if (Integer.decode(value) == 0 || Integer.decode(value) == 1 || Integer.decode(value) == 2) {
                param.chains = Integer.decode(value);
            } else {
                throw new RuntimeException("Parameter " + STRAND + " should be either 0, 1 or 2");
            }
        }

        if ((value = cl.getOptionValue(INPUT_FASTQ)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_LINE)) != null) {
            param.inputFqLinePath = value;
            param.inputFqPath = value;
        } else {
            help.printHelp();
            System.exit(0);
            //throw new IOException("Input query file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_FILE)) != null) {
            param.outputPath = value;
        } else {
            info.readMessage("Output file not set of -outfile options");
            info.screenDump();
        }

        if ((value = cl.getOptionValue(INPUT_REF)) != null) {
            param.inputFaPath = new File(value).getAbsolutePath();
        } else {
            info.readMessage("Input reference file had not specified.");
            info.screenDump();
        }

        File inputFasta = new File(param.inputFaPath).getAbsoluteFile();
        if (!inputFasta.exists()) {
            info.readMessage("Input reference file had not found.");
            info.screenDump();
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        if (param.inputFqPath.endsWith(".gz")) {
        }

        param.bestNas = (param.alignLength * param.readIdentity) / 100;
        param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

        if (param.bestKmers < (param.kmerSize - 3)) {
            param.bestKmers = param.kmerSize - 3;
        }

        if (param.maskRepeat == 0) {
            param.validNt = param.validNtNomask;
            param.invalidNt = param.nxNomask;
        }

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();//from   w  w w.j a v a 2s.com

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(COLUMN)) != null) {
            param.columns = value;
            param.columnStart = Integer.decode(value.split("-")[0]);
            param.columnEnd = Integer.decode(value.split("-")[1]);
        } else {
            param.columnStart = Integer.decode(param.columns.split("-")[0]);
            param.columnEnd = Integer.decode(param.columns.split("-")[1]);
        }

        if ((value = cl.getOptionValue(COLUMN2)) != null) {
            param.columns2 = value;
            param.column2Start = Integer.decode(value.split("-")[0]);
            param.column2End = Integer.decode(value.split("-")[1]);
        } else {
            param.column2Start = Integer.decode(param.columns.split("-")[0]);
            param.column2End = Integer.decode(param.columns.split("-")[1]);
        }

        if (cl.hasOption(CACHE)) {
            param.cache = true;
        }

        if ((value = cl.getOptionValue(INPUT_VCF)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_TAB)) != null) {
            param.inputFqPath = value;
        } else {
            help.printStatisticerHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printStatisticerHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();//from  ww w  .j  av  a  2s. c o  m

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(WINDOW)) != null) {
            param.window = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(COLUMN)) != null) {
            param.columns = value;
            param.columnStart = Integer.decode(value.split("-")[0]);
            param.columnEnd = Integer.decode(value.split("-")[1]);
        } else {
            param.columnStart = Integer.decode(param.columns.split("-")[0]);
            param.columnEnd = Integer.decode(param.columns.split("-")[1]);
        }

        if (cl.hasOption(CACHE)) {
            param.cache = true;
        }

        if ((value = cl.getOptionValue(MODELS)) != null) {
            param.model = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(CLUSTER)) != null) {
            param.clusterNum = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(ITERATION)) != null) {
            param.iterationNum = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_VCF)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_TAB)) != null) {
            param.inputFqPath = value;
        } else {
            help.printStatisticerHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printStatisticerHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();//from  w ww  .  j av  a 2s  .  co  m

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printConverterHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printConverterHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_FASTQ)) != null) {
            param.inputFqPath = value;
        } else {
            help.printConverterHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        if ((value = cl.getOptionValue(OUTPUT_FORMAT)) != null) {
            param.outputformat = Integer.decode(value);
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            info.readMessage("Output file not set of -outfile options");
            info.screenDump();
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        // param.bestNas = (param.alignLength * param.readIdentity) / 100;
        // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();//from   w  ww.j  a v a 2  s  .  c  om

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(COLUMN)) != null) {
            param.columns = value;
            param.columnStart = Integer.decode(value.split("-")[0]);
            param.columnEnd = Integer.decode(value.split("-")[1]);
        } else {
            param.columnStart = Integer.decode(param.columns.split("-")[0]);
            param.columnEnd = Integer.decode(param.columns.split("-")[1]);
        }

        if (cl.hasOption(CACHE)) {
            param.cache = true;
        }

        if ((value = cl.getOptionValue(INPUT_VCF)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_TAB)) != null) {
            param.inputFqPath = value;
        } else {
            help.printStatisticerHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printStatisticerHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();/*from  w  w w. j  a v a2  s  . c o  m*/

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printDecompresserHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printDecompresserHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_FASTQ)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_LINE)) != null) {
            param.inputFqLinePath = value;
            param.inputFqPath = value;
        } else {
            help.printDecompresserHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printDecompresserHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        if (cl.hasOption(FASTQ_FILTER)) {
            param.filterFastq = true;
        }

        if (cl.hasOption(FASTA_CONVERT)) {
            param.filterToFasta = true;
        }

        if (cl.hasOption(LINE_FASTA)) {
            param.lineToFasta = true;
        }

        // param.bestNas = (param.alignLength * param.readIdentity) / 100;
        // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();// w w  w  .  j a v a 2  s .  c  om

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printScriptPiperHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printScriptPiperHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_NODES)) != null) {
            param.inputNodes = Integer.decode(value);
        } else {
            help.printScriptPiperHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printScriptPiperHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        if ((value = cl.getOptionValue(INPUT_TOOL)) != null) {
            param.tool = value.replaceAll("\"", "");
            info.readParagraphedMessages("External tool locate at : \n\t" + param.tool
                    + "\nplease ensure that all nodes have such tools in the same path.\nOr it is located in a shared file system.\nOr use a Docker container");
            info.screenDump();
        } else {
            help.printScriptPiperHelp();
            info.readMessage("External tool path have not been set with parameter -tool");
            info.screenDump();
            System.exit(0);
        }

        if ((value = cl.getOptionValue(TOOL_DEPEND)) != null) {
            param.toolDepend = value.replaceAll("\"", "");
            info.readParagraphedMessages("External tool Dependencies : \n\t" + param.toolDepend + "\n");
            info.screenDump();
        } else {
            info.readMessage(
                    "External tool dependencies have not been set, will run with tool build-in Interpreter");
            info.screenDump();
        }

        if ((value = cl.getOptionValue(TOOL_PARAM)) != null) {
            param.toolParam = value.replaceAll("\"", "");
            info.readParagraphedMessages("External tool parameter : \n\t" + param.toolParam
                    + "\nThe entire command looks like : \n\t" + param.toolDepend + " " + param.tool + " "
                    + param.toolParam);
            info.screenDump();
            info.readParagraphedMessages("Final external command is : \n\t" + param.toolDepend + " "
                    + param.tool + " " + param.toolParam);
            info.screenDump();
        } else {
            info.readMessage("External tool parameter have not been set, will run with its default parameter");
            info.screenDump();
        }

        // param.bestNas = (param.alignLength * param.readIdentity) / 100;
        // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();/* ww  w.  ja  v  a 2 s.  c o  m*/

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(WINDOW)) != null) {
            param.window = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(COLUMN)) != null) {
            param.columns = value;
            param.columnStart = Integer.decode(value.split("-")[0]);
            param.columnEnd = Integer.decode(value.split("-")[1]);
        } else {
            param.columnStart = Integer.decode(param.columns.split("-")[0]);
            param.columnEnd = Integer.decode(param.columns.split("-")[1]);
        }

        if (cl.hasOption(CACHE)) {
            param.cache = true;
        }

        if ((value = cl.getOptionValue(COMPO)) != null) {
            param.componentNum = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_VCF)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_TAB)) != null) {
            param.inputFqPath = value;
        } else {
            help.printStatisticerHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printStatisticerHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();/*w  w w.  j a  v a  2 s  .co  m*/

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printStatisticerHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(WINDOW)) != null) {
            param.window = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(COLUMN)) != null) {
            param.columns = value;
            param.columnStart = Integer.decode(value.split("-")[0]);
            param.columnEnd = Integer.decode(value.split("-")[1]);
        } else {
            param.columnStart = Integer.decode(param.columns.split("-")[0]);
            param.columnEnd = Integer.decode(param.columns.split("-")[1]);
        }

        if (cl.hasOption(CACHE)) {
            param.cache = true;
        }

        if ((value = cl.getOptionValue(MODELS)) != null) {
            param.model = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(ITERATION)) != null) {
            param.iterationNum = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_VCF)) != null) {
            param.inputFqPath = value;
        } else if ((value = cl.getOptionValue(INPUT_TAB)) != null) {
            param.inputFqPath = value;
        } else {
            help.printStatisticerHelp();
            System.exit(0);
            //                throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        if ((value = cl.getOptionValue(INPUT_TRAIN)) != null) {
            param.inputTrainPath = value;
        } else {
            help.printStatisticerHelp();
            System.exit(0);
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) {
            param.outputPath = value;
        } else {
            help.printStatisticerHelp();
            info.readMessage("Output file not set with -outfile options");
            info.screenDump();
            System.exit(0);
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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

public DefaultParam importCommandLine() {

    /* Assigning Parameter ID to an ascending number */
    putParameterID();/*ww w . java  2s .  c  o  m*/

    /* Assigning parameter descriptions to each parameter ID */
    addParameterInfo();

    /* need a Object parser of PosixParser class for the function parse of CommandLine class */
    PosixParser parser = new PosixParser();

    /* print out help information */
    HelpParam help = new HelpParam(parameter, parameterMap);

    /* check each parameter for assignment */
    try {
        long input_limit = -1;
        int threads = Runtime.getRuntime().availableProcessors();

        /* Set Object cl of CommandLine class for Parameter storage */
        CommandLine cl = parser.parse(parameter, arguments, true);
        if (cl.hasOption(HELP)) {
            help.printReporterHelp();
            System.exit(0);
        }

        if (cl.hasOption(HELP2)) {
            help.printReporterHelp();
            System.exit(0);
        }

        if (cl.hasOption(VERSION)) {
            System.exit(0);
        }

        /* Checking all parameters */

        String value;

        if ((value = cl.getOptionValue(PARTITIONS)) != null) {
            param.partitions = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_KEY)) != null) {
            param.word = value;
        }

        if ((value = cl.getOptionValue(INPUT_VALUE)) != null) {
            param.count = Integer.decode(value);
        }

        if ((value = cl.getOptionValue(INPUT_HIT)) != null) {
            param.inputResultPath = value;
        } else {
            help.printReporterHelp();
            System.exit(0);
            // throw new IOException("Input file not specified.\nUse -help for list of options");
        }

        /* not applicable for HDFS and S3 */
        /* using TextFileBufferInput for such purpose */
        //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
        //         if (!inputFastq.exists()){
        //            err.println("Input query file not found.");
        //            return;
        //i         }

        if ((value = cl.getOptionValue(OUTPUT_REPORT)) != null) {
            param.outputPath = value;
        } else {
            info.readMessage("Output file not set of -outfile options");
            info.screenDump();
        }

        File outfile = new File(param.outputPath).getAbsoluteFile();
        if (outfile.exists()) {
            info.readParagraphedMessages(
                    "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
            info.screenDump();
            Runtime.getRuntime().exec("rm -rf " + param.outputPath);
        }

        // param.bestNas = (param.alignLength * param.readIdentity) / 100;
        // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

    } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (RuntimeException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    } catch (ParseException e) {
        info.readMessage("Parameter settings incorrect.");
        info.screenDump();
        e.printStackTrace();
        System.exit(0);
    }

    return param;
}

---

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