org.vetmeduni.tools.cmd.CommonOptions.java Source code

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Here is the source code for org.vetmeduni.tools.cmd.CommonOptions.java

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/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2015 Daniel Gmez-Snchez
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 */
package org.vetmeduni.tools.cmd;

import htsjdk.samtools.util.Log;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.vetmeduni.tools.ToolNames;

import static org.vetmeduni.tools.cmd.OptionUtils.getUniqueValue;

/**
 * Class that contains static instances of common options and their checking
 *
 * @author Daniel Gmez-Snchez
 */
public class CommonOptions {

    /**
     * Default number of threads for multi-threaded input
     */
    public static final int DEFAULT_THREADS = 1;

    /**
     * Option for maintain the format instead of standardize
     */
    public static final Option maintainFormat = Option.builder("nstd").longOpt("no-standardize-output").desc(
            "By default, the output of this program is encoding in Sanger. If you disable this behaviour, the format of the output will be the same as the input (not recommended)")
            .hasArg(false).optionalArg(true).build();

    /**
     * Option for disable zipped output for FASTQ outputs
     */
    public static final Option disableZippedOutput = Option.builder("dgz").longOpt("disable-zipped-output")
            .desc("Disable zipped output").hasArg(false).optionalArg(true).build();

    /**
     * Option for parallelization. Currently is not really multi-thread
     */
    // TODO: change the description when real multi-thread
    public static final Option parallel = Option.builder("nt").longOpt("number-of-thread").desc(
            "Specified the number of threads to use. Warning: real multi-thread is not implemented; if using more than one thread the option is a switch and the number of threads depends on the number of outputs. [Default="
                    + DEFAULT_THREADS + "]")
            .hasArg().numberOfArgs(1).argName("INT").optionalArg(true).build();

    /**
     * Check if the command line provides the maintain format option and log into the logger
     *
     * @param logger the logger where output the information
     * @param cmd    the command line where check if the option is set
     *
     * @return <code>true</code> if the format is maintained; <code>false</code> if it should be standardize
     */
    public static boolean isMaintained(Log logger, CommandLine cmd) {
        if (cmd.hasOption(maintainFormat.getOpt())) {
            logger.warn("Output will not be standardize. Does not provide the option -", maintainFormat.getOpt(),
                    " to avoid this behaviour");
            return true;
        } else {
            logger.info("Output will be in Sanger format independently of the input format");
            return false;
        }
    }

    /**
     * Check if the command line provides an option for disable zipping
     *
     * @param cmd the command line where check if the option is set
     *
     * @return <code>true</code> if gzip is disable; <code>false</code> otherwise
     */
    public static boolean isZipDisable(CommandLine cmd) {
        return cmd.hasOption(disableZippedOutput.getOpt());
    }

    /**
     * Get the default number of threads if the command line does not contain the parallel option; if it is contain,
     * parse the command line and return the number of threads asked for
     *
     * @param cmd the command line where check if the option is set
     *
     * @return the number of threads to use
     * @throws org.vetmeduni.tools.ToolNames.ToolException if the option is not numeric
     */
    public static int numberOfThreads(Log logger, CommandLine cmd) {
        try {
            int nThreads = DEFAULT_THREADS;
            if (cmd.hasOption(parallel.getOpt())) {
                nThreads = Integer.parseInt(getUniqueValue(cmd, parallel.getOpt()));
                if (nThreads != 1) {
                    // TODO: change when real multi-thread is implemented
                    logger.warn(
                            "Currently multi-threads does not control the number of threads in use, depends on the number of outputs");
                } else if (nThreads < 0) {
                    throw new NumberFormatException();
                }
            }
            return nThreads;
        } catch (NumberFormatException e) {
            throw new ToolNames.ToolException("--" + parallel.getLongOpt() + " should be a positive integer");
        }
    }
}