it.crs4.seal.recab.RecabTableOptionParser.java Source code

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Here is the source code for it.crs4.seal.recab.RecabTableOptionParser.java

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// Copyright (C) 2011-2012 CRS4.
//
// This file is part of Seal.
//
// Seal is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// Seal is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License along
// with Seal.  If not, see <http://www.gnu.org/licenses/>.

package it.crs4.seal.recab;

import it.crs4.seal.common.SealToolParser;
import it.crs4.seal.common.ClusterUtils;

import java.util.ArrayList;
import java.io.IOException;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;

import org.apache.commons.cli.*;

public class RecabTableOptionParser extends SealToolParser {

    public static final String ConfigSection = "RecabTable";

    private Option vcfFileOpt;
    private Path vcfFilePath;

    private Option rodFileOpt;
    private Path rodFilePath;

    private Configuration conf;

    @SuppressWarnings("static") // for OptionBuilder
    public RecabTableOptionParser() {
        super(ConfigSection, "seal recab_table");

        // define the options
        vcfFileOpt = OptionBuilder.withDescription("VCF file with known variation sites").hasArg()
                .withArgName("FILE").withLongOpt("vcf-file").create("vcf");
        options.addOption(vcfFileOpt);

        rodFileOpt = OptionBuilder.withDescription("ROD file with known variation sites").hasArg()
                .withArgName("FILE").withLongOpt("rod-file").create("rod");
        options.addOption(rodFileOpt);

        this.setMinReduceTasks(1);
        this.setAcceptedInputFormats(new String[] { "bam", "sam" });
        conf = null;
    }

    @Override
    protected CommandLine parseOptions(Configuration conf, String[] args) throws IOException, ParseException {
        if (conf == null)
            throw new NullPointerException("null conf provided");

        this.conf = conf;

        CommandLine line = super.parseOptions(conf, args);

        if (line.hasOption(vcfFileOpt.getOpt()) && line.hasOption(rodFileOpt.getOpt()))
            throw new ParseException("You can't specify both VCF (" + vcfFileOpt.getLongOpt() + ") and ROD ("
                    + rodFileOpt.getLongOpt() + ") files.  Please specify one or the other.");

        if (line.hasOption(vcfFileOpt.getOpt())) {
            vcfFilePath = new Path(line.getOptionValue(vcfFileOpt.getOpt()));
            if (!vcfFilePath.getFileSystem(conf).exists(vcfFilePath))
                throw new ParseException("File " + vcfFilePath + " doesn't exist");
        } else if (line.hasOption(rodFileOpt.getOpt())) {
            rodFilePath = new Path(line.getOptionValue(rodFileOpt.getOpt()));
            if (!rodFilePath.getFileSystem(conf).exists(rodFilePath))
                throw new ParseException("File " + rodFilePath + " doesn't exist");
        } else
            throw new ParseException(
                    "You must specify a file with known genetic variation sites (either VCF or ROD).");

        // set number of reduce tasks to use
        conf.set(ClusterUtils.NUM_RED_TASKS_PROPERTY, String.valueOf(getNReduceTasks()));
        return line;
    }

    public Path getVcfFile() {
        return vcfFilePath;
    }

    public Path getRodFile() {
        return rodFilePath;
    }
}