package org.broadinstitute.sting.gatk.refdata.features.table;

import org.broad.tribble.Feature;
import org.broad.tribble.readers.LineReader;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;

/**
 * Created by IntelliJ IDEA.
 * User: chartl
 * Date: 3/28/11
 * Time: 2:47 PM
 * To change this template use File | Settings | File Templates.
 */
/**
 * The standard table codec with a slightly different parsing convention (expects loci as contig start stop, not contig:start-stop)
 */
public class BedTableCodec extends TableCodec implements ReferenceDependentFeatureCodec {

    @Override
    public Feature 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);
    }
}