fi.tkk.ics.hadoop.bam.cli.CLIMRBAMPlugin.java Source code

Introduction

Here is the source code for fi.tkk.ics.hadoop.bam.cli.CLIMRBAMPlugin.java

Source

// Copyright (c) 2013 Aalto University
//
// 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 SOFTWARE.

// File created: 2013-06-20 14:22:25

package fi.tkk.ics.hadoop.bam.cli;

import java.util.ArrayList;
import java.util.List;
import java.util.Locale;

import org.apache.hadoop.conf.Configuration;

import fi.tkk.ics.hadoop.bam.custom.jargs.gnu.CmdLineParser;
import static fi.tkk.ics.hadoop.bam.custom.jargs.gnu.CmdLineParser.Option.*;

import fi.tkk.ics.hadoop.bam.AnySAMInputFormat;
import fi.tkk.ics.hadoop.bam.AnySAMOutputFormat;
import fi.tkk.ics.hadoop.bam.KeyIgnoringAnySAMOutputFormat;
import fi.tkk.ics.hadoop.bam.SAMFormat;
import fi.tkk.ics.hadoop.bam.cli.CLIMRPlugin;
import fi.tkk.ics.hadoop.bam.util.Pair;

/** Like CLIMRPlugin, with added useful defaults for plugins working solely on
 * BAM/SAM files.
 *
 * Adds an option description for the "-o" option in CLIMRPlugin, so subclasses
 * shouldn't.
 */
public abstract class CLIMRBAMPlugin extends CLIMRPlugin {
    protected SAMFormat samFormat = null;

    private static final List<Pair<CmdLineParser.Option, String>> optionDescs = new ArrayList<Pair<CmdLineParser.Option, String>>();

    protected static final CmdLineParser.Option formatOpt = new StringOption('F', "format=FMT"),
            noTrustExtsOpt = new BooleanOption("no-trust-exts");

    protected CLIMRBAMPlugin(String commandName, String description, String version, String usageParams,
            List<Pair<CmdLineParser.Option, String>> optionDescs, String longDescription) {
        // "call to super must be first statement in constructor" so you get that
        // lovely expression instead of two simple statements.
        super(commandName, description, version, usageParams,
                optionDescs == null ? CLIMRBAMPlugin.optionDescs
                        : (optionDescs.addAll(CLIMRBAMPlugin.optionDescs) ? optionDescs : optionDescs),
                longDescription);
    }

    static {
        optionDescs.add(new Pair<CmdLineParser.Option, String>(noTrustExtsOpt,
                "detect SAM/BAM files only by contents, " + "never by file extension"));
        optionDescs.add(new Pair<CmdLineParser.Option, String>(formatOpt,
                "select the output format based on FMT: SAM or BAM"));

        optionDescs.add(new Pair<CmdLineParser.Option, String>(outputPathOpt,
                "output a complete SAM/BAM file to the file PATH, "
                        + "removing the parts from WORKDIR; SAM/BAM is chosen "
                        + "by file extension, if appropriate (but -F takes " + "precedence)"));
    }

    /** Should be called before accessing any of the protected data such as
     * samFormat.
     */
    @Override
    public boolean cacheAndSetProperties(CmdLineParser parser) {
        if (!super.cacheAndSetProperties(parser))
            return false;

        if (!cacheSAMFormat(parser))
            return false;

        final Configuration conf = getConf();

        conf.setBoolean(AnySAMInputFormat.TRUST_EXTS_PROPERTY, !parser.getBoolean(noTrustExtsOpt));

        // Let the output format know if we're going to merge the output, so that
        // it doesn't write headers into the intermediate files.
        conf.setBoolean(KeyIgnoringAnySAMOutputFormat.WRITE_HEADER_PROPERTY, outPath == null);

        return true;
    }

    private boolean cacheSAMFormat(CmdLineParser parser) {
        final String f = (String) parser.getOptionValue(formatOpt);
        if (f != null) {
            try {
                samFormat = SAMFormat.valueOf(f.toUpperCase(Locale.ENGLISH));
            } catch (IllegalArgumentException e) {
                System.err.printf("%s :: invalid format '%s'\n", getCommandName(), f);
                return false;
            }
        }
        if (samFormat == null)
            samFormat = outPath == null ? SAMFormat.BAM : SAMFormat.inferFromFilePath(outPath);

        getConf().set(AnySAMOutputFormat.OUTPUT_SAM_FORMAT_PROPERTY, samFormat.toString());
        return true;
    }
}