it.crs4.seal.demux.DemuxOptionParser.java Source code

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Here is the source code for it.crs4.seal.demux.DemuxOptionParser.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.demux;

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

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 DemuxOptionParser extends SealToolParser {

    public static final String ConfigSection = "Demux";

    private Option sampleSheetOpt;
    private Path sampleSheetPath;

    private Option laneContentOpt;
    private boolean createLaneContent;

    private Option maxTagMismatchesOpt;
    private int maxTagMismatches;

    private Option noIndexReadsOpt;
    private boolean noIndexReads;

    private Option separateReadsOpt;
    private boolean separateReads;

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

        sampleSheetOpt = OptionBuilder.withDescription("Sample sheet for the experiment").hasArg()
                .withArgName("FILE").withLongOpt("sample-sheet").create("s");
        options.addOption(sampleSheetOpt);

        laneContentOpt = OptionBuilder.withDescription("create LaneContent files")
                .withLongOpt("create-lane-content").create("l");
        createLaneContent = false;
        options.addOption(laneContentOpt);

        maxTagMismatchesOpt = OptionBuilder
                .withDescription("Maximum number of acceptable barcode substitution errors (default: 0)").hasArg()
                .withArgName("N").withLongOpt("mismatches").create("m");
        maxTagMismatches = 0; // default value
        options.addOption(maxTagMismatchesOpt);

        noIndexReadsOpt = OptionBuilder
                .withDescription("Dataset doesn't contain index reads.  Sort reads only by lane (default: false)")
                .withLongOpt("no-index").create("ni");
        noIndexReads = false; // default value
        options.addOption(noIndexReadsOpt);

        separateReadsOpt = OptionBuilder
                .withDescription("Generate separate directories for each read number (default: false)")
                .withLongOpt("separate-reads").create("sepr");
        separateReads = false; // default value
        options.addOption(separateReadsOpt);

        this.setMinReduceTasks(1);
        this.setAcceptedInputFormats(new String[] { "qseq", "fastq" });
        this.setAcceptedOutputFormats(new String[] { "qseq", "fastq" });
    }

    @Override
    protected CommandLine parseOptions(Configuration conf, String[] args) throws IOException, ParseException {
        CommandLine line = super.parseOptions(conf, args);
        // options
        if (line.hasOption(sampleSheetOpt.getOpt())) {
            sampleSheetPath = new Path(line.getOptionValue(sampleSheetOpt.getOpt()));
            if (sampleSheetPath.getFileSystem(conf).exists(sampleSheetPath))
                sampleSheetPath = sampleSheetPath.makeQualified(sampleSheetPath.getFileSystem(conf));
            else
                throw new ParseException("Sample sheet " + sampleSheetPath.toString() + " doesn't exist");
        } else
            throw new ParseException("Missing --" + sampleSheetOpt.getLongOpt() + " argument");

        if (line.hasOption(laneContentOpt.getOpt()))
            createLaneContent = true;

        if (line.hasOption(maxTagMismatchesOpt.getOpt())) {
            String s = line.getOptionValue(maxTagMismatchesOpt.getOpt());
            try {
                maxTagMismatches = Integer.parseInt(s);
                if (maxTagMismatches < 0)
                    throw new ParseException(
                            "Maximum number of acceptable barcode mismatches must be greater than zero (got " + s
                                    + ")");
                conf.set(Demux.CONF_MAX_MISMATCHES, String.valueOf(maxTagMismatches));
            } catch (NumberFormatException e) {
                throw new ParseException("Invalid number '" + s + "' for " + maxTagMismatchesOpt.getLongOpt());
            }
        }

        if (line.hasOption(noIndexReadsOpt.getOpt()))
            noIndexReads = true;

        if (line.hasOption(separateReadsOpt.getOpt()))
            separateReads = true;

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

    public Path getSampleSheetPath() {
        return sampleSheetPath;
    }

    public boolean getCreateLaneContent() {
        return createLaneContent;
    }

    public int getMaxTagMismatches() {
        return maxTagMismatches;
    }

    public boolean getNoIndexReads() {
        return noIndexReads;
    }

    public boolean getSeparateReads() {
        return separateReads;
    }
}