it.crs4.seal.read_sort.ReadSortOptionParser.java Source code

Introduction

Here is the source code for it.crs4.seal.read_sort.ReadSortOptionParser.java

Source

// 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.read_sort;

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 ReadSortOptionParser extends SealToolParser {

    public static final String ConfigSection = "ReadSort";

    private Option ann;
    private Option distReference;

    @SuppressWarnings("static") // for OptionBuilder
    public ReadSortOptionParser() {
        super(ConfigSection, "seal_read_sort");

        // define the custom options
        ann = OptionBuilder
                .withDescription("annotation file (.ann) of the BWA reference used to create the SAM data").hasArg()
                .withArgName("ref.ann").withLongOpt("annotations").create("ann");
        options.addOption(ann);

        distReference = OptionBuilder
                .withDescription(
                        "BWA reference on HDFS used to create the SAM data, to be distributed by DistributedCache")
                .hasArg().withArgName("archive").withLongOpt("distributed-reference").create("distref");
        options.addOption(distReference);

        this.setMinReduceTasks(1);
    }

    @Override
    protected CommandLine parseOptions(Configuration conf, String[] args) throws IOException, ParseException {
        CommandLine line = super.parseOptions(conf, args);

        /********* distributed reference and annotations *********/
        if (line.hasOption(distReference.getOpt())) {
            // Distribute the reference archive, and create a // symlink "reference" to the directory
            Path optPath = new Path(line.getOptionValue(distReference.getOpt()));
            optPath = optPath.makeQualified(optPath.getFileSystem(conf));
            Path cachePath = new Path(optPath.toString() + "#reference");
            conf.set("mapred.cache.archives", cachePath.toString());
            conf.set("mapred.create.symlink", "yes");

            if (line.hasOption(ann.getOpt()))
                conf.set(ReadSort.REF_ANN_PROP_NAME, "reference/" + line.getOptionValue(ann.getOpt()));
            else
                throw new ParseException(
                        "You must specify the name of the annotation file within the distributed reference archive with -"
                                + ann.getOpt());
        } else if (line.hasOption(ann.getOpt())) {
            // direct access to the reference annotation
            conf.set(ReadSort.REF_ANN_PROP_NAME, line.getOptionValue(ann.getOpt()));
        } else
            throw new ParseException("You must provide the path the reference annotation file (<ref>.ann)");

        conf.set(ClusterUtils.NUM_RED_TASKS_PROPERTY, String.valueOf(getNReduceTasks()));
        return line;
    }
}