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Next generation sequencing (NGS/HTS) command line tools.
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/*

    ngs-tools  Next generation sequencing (NGS/HTS) command line tools.
    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)

    This library is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published
    by the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.

    This library is distributed in the hope that it will be useful, but WITHOUT
    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
    License for more details.

    You should have received a copy of the GNU Lesser General Public License
    along with this library;  if not, write to the Free Software Foundation,
    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.

    > http://www.gnu.org/licenses/lgpl.html

*/
package org.nmdp.ngs.tools;

import static com.google.common.base.Preconditions.checkNotNull;

import static org.dishevelled.compress.Readers.reader;
import static org.dishevelled.compress.Writers.writer;

import java.io.BufferedReader;
import java.io.File;
import java.io.PrintWriter;
import java.io.IOException;

import java.util.HashMap;
import java.util.Map;

import java.util.concurrent.Callable;

import org.dishevelled.commandline.ArgumentList;
import org.dishevelled.commandline.CommandLine;
import org.dishevelled.commandline.CommandLineParseException;
import org.dishevelled.commandline.CommandLineParser;
import org.dishevelled.commandline.Switch;
import org.dishevelled.commandline.Usage;

import org.dishevelled.commandline.argument.FileArgument;

import org.nmdp.ngs.align.BedListener;
import org.nmdp.ngs.align.BedReader;
import org.nmdp.ngs.align.BedRecord;
import org.nmdp.ngs.align.BedWriter;

/**
 * Liftover BED file.
 */
public final class LiftoverBed implements Callable {
    private final File refBedFile;
    private final File sourceBedFile;
    private final File targetBedFile;
    private static final String USAGE = "ngs-liftover-bed -r ref.bed.gz [args]";


    /**
     * Liftover BED file.
     *
     * @param refBedFile reference BED file, must not be null
     * @param sourceBedFile source BED file, if any
     * @param targetBedFile target BED file, if any
     */
    public LiftoverBed(final File refBedFile, final File sourceBedFile, final File targetBedFile) {
        checkNotNull(refBedFile);
        this.refBedFile = refBedFile;
        this.sourceBedFile = sourceBedFile;
        this.targetBedFile = targetBedFile;
    }


    @Override
    public Integer call() throws Exception {
        BufferedReader reader = null;
        PrintWriter writer = null;
        try {
            reader = reader(sourceBedFile);
            writer = writer(targetBedFile);

            final PrintWriter w = writer;
            final Map ref = readRefFile();
            BedReader.stream(reader, new BedListener() {
                    @Override
                    public boolean record(final BedRecord source) {
                        BedRecord target = ref.get(source.chrom());

                        if (target != null) {
                            BedRecord lifted = new BedRecord(target.chrom(),
                                                             target.start() + source.start(),
                                                             target.start() + source.start() + (source.end() - source.start()),
                                                             source.name());

                            BedWriter.write(lifted, w);
                        }
                        return true;
                    }
                });

            return 0;
        }
        finally {
            try {
                reader.close();
            }
            catch (Exception e) {
                // empty
            }
            try {
                writer.close();
            }
            catch (Exception e) {
                // empty
            }
        }
    }

    private Map readRefFile() throws IOException {
        BufferedReader reader = null;
        final Map ref = new HashMap(10000);
        try {
            reader = reader(refBedFile);

            BedReader.stream(reader, new BedListener() {
                    @Override
                    public boolean record(final BedRecord rec) {
                        BedRecord prev = ref.put(rec.name(), rec);
                        if (prev != null) {
                            // warn non-unique mapping
                        }
                        return true;
                    }
                });
        }
        finally {
            try {
                reader.close();
            }
            catch (Exception e) {
                // empty
            }
        }
        return ref;
    }


    /**
     * Main.
     *
     * @param args command line args
     */
    public static void main(final String[] args) {
        Switch about = new Switch("a", "about", "display about message");
        Switch help = new Switch("h", "help", "display help message");
        FileArgument refBedFile = new FileArgument("r", "ref-bed-file", "reference BED file", true);
        FileArgument sourceBedFile = new FileArgument("i", "source-bed-file", "input BED file, default stdin", false);
        FileArgument targetBedFile = new FileArgument("o", "target-bed-file", "output BED file, default stdout", false);

        ArgumentList arguments = new ArgumentList(about, help, refBedFile, sourceBedFile, targetBedFile);
        CommandLine commandLine = new CommandLine(args);

        LiftoverBed liftoverBed = null;
        try {
            CommandLineParser.parse(commandLine, arguments);
            if (about.wasFound()) {
                About.about(System.out);
                System.exit(0);
            }
            if (help.wasFound()) {
                Usage.usage(USAGE, null, commandLine, arguments, System.out);
                System.exit(0);
            }
            liftoverBed = new LiftoverBed(refBedFile.getValue(), sourceBedFile.getValue(), targetBedFile.getValue());
        }
        catch (CommandLineParseException e) {
            if (about.wasFound()) {
                About.about(System.out);
                System.exit(0);
            }
            if (help.wasFound()) {
                Usage.usage(USAGE, null, commandLine, arguments, System.out);
                System.exit(0);
            }
            Usage.usage(USAGE, e, commandLine, arguments, System.err);
            System.exit(-1);
        }
        try {
            System.exit(liftoverBed.call());
        }
        catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }
    }
}