IntervalListToBed.java

/*
 * The MIT License
 *
 * Copyright (c) 2016 Tim Fennell
 *
 * 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.
 */
package picard.util;

import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.RuntimeIOException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.Intervals;

import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.stream.Collectors;

/**
 * Trivially simple command line program to convert an IntervalList file to a BED file.
 * @author Tim Fennell
 */
@CommandLineProgramProperties(
        usage = "Converts an Picard IntervalList file to a BED file.",
        usageShort = "Converts an Picard IntervalList file to a BED file.",
        programGroup = Intervals.class
)
public class IntervalListToBed extends CommandLineProgram {
    @Option(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME, doc="Input IntervalList file.")
    public File INPUT;

    @Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="Output BED file.")
    public File OUTPUT;

    @Option(doc="The score, between 0-1000, to output for each interval in the BED file.")
    public int SCORE = 500;

    @Option(doc="If true, sort the interval list prior to outputting as BED file.")
    public boolean SORT = true;

    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

        IntervalList intervals = IntervalList.fromFile(INPUT);
        if (SORT) intervals = intervals.sorted();

        try {
            final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);
            for (final Interval i : intervals) {
                final String strand = i.isNegativeStrand() ? "-" : "+";
                final List<?> fields = CollectionUtil.makeList(i.getContig(), i.getStart()-1, i.getEnd(), i.getName(), SCORE, strand);
                out.append(fields.stream().map(String::valueOf).collect(Collectors.joining("\t")));
                out.newLine();
            }

            out.close();
        }
        catch (IOException ioe) {
            throw new RuntimeIOException(ioe);
        }

        return 0;
    }
}