/*
* Copyright 2012-2015 Broad Institute, Inc.
* 
* 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 org.broadinstitute.gatk.utils.codecs.table;

import org.broadinstitute.gatk.utils.refdata.ReferenceDependentFeatureCodec;

import java.util.Arrays;

/**
 * The standard table codec that expects loci as contig start stop, not contig:start-stop
 *
 * <p>
 * The standard table codec with a slightly different parsing convention
 * (expects loci as contig start stop, not contig:start-stop)
 * </p>
 *
 * <p>
 * See also: TableCodec
 * </p>
 *
 * @author Chris Hartl
 * @since 2010
 */
public class BedTableCodec extends TableCodec implements ReferenceDependentFeatureCodec {

    @Override
    public TableFeature decode(String line) {
        if (line.startsWith(headerDelimiter) || line.startsWith(commentDelimiter) || line.startsWith(igvHeaderDelimiter))
            return null;
        String[] split = line.split(delimiterRegex);
        if (split.length < 1)
            throw new IllegalArgumentException("TableCodec line = " + line + " doesn't appear to be a valid table format");
        return new TableFeature(genomeLocParser.createGenomeLoc(split[0],Integer.parseInt(split[1])-1,Integer.parseInt(split[2])), Arrays.asList(split),header);
    }
}