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 *
 * Copyright (c) 2007-2015 Broad Institute
 *
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 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
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 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
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 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
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 *
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 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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package org.broad.igv.tools.converters;

import org.broad.igv.feature.*;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.GFFCodec;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.Feature;
import org.junit.Test;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.List;

import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;

/**
 * @author Jim Robinson
 * @date 2/15/12
 */
public class GFFtoBedTest {


    @Test
    public void testConvert() throws Exception {

        File inputFile = new File(TestUtils.DATA_DIR, "gff/gene.unsorted.gff3");
        File outputFile = new File(TestUtils.TMP_OUTPUT_DIR, "gene.bed");
        outputFile.deleteOnExit();

        // Convert
        GFFtoBed.convert(inputFile, outputFile);

        // Now compare features from both files, they should be identical

        BufferedReader gffReader = null;
        BufferedReader bedReader = null;
        try {
            Genome genome = null; // Not needed for this test
            gffReader = new BufferedReader(new FileReader(inputFile));
            GFFParser parser = new GFFParser();
            GFFCodec.Version version = inputFile.getPath().endsWith(".gff3") ? GFFCodec.Version.GFF3 : GFFCodec.Version.GFF2;
            GFFCodec codec = new GFFCodec(version, null);
            List<Feature> gffFeatures = parser.loadFeatures(gffReader, genome, codec);

            bedReader = new BufferedReader(new FileReader(outputFile));
            FeatureParser bedParser = AbstractFeatureParser.getInstanceFor(new ResourceLocator(outputFile.getAbsolutePath()), null);
            List<Feature> bedFeatures = bedParser.loadFeatures(bedReader, genome);

            assertTrue(gffFeatures.size() > 0);
            assertEquals(gffFeatures.size(), bedFeatures.size());
            for (int i = 0; i < gffFeatures.size(); i++) {
                BasicFeature gffFeature = (BasicFeature) gffFeatures.get(i);
                BasicFeature bedFeature = (BasicFeature) bedFeatures.get(i);

                compare(gffFeature, bedFeature);

            }

        } finally {
            gffReader.close();
        }


    }

    private void compare(BasicFeature gffFeature, BasicFeature bedFeature) {

        assertEquals(gffFeature.getChr(), bedFeature.getChr());
        assertEquals(gffFeature.getStart(), bedFeature.getStart());
        assertEquals(gffFeature.getEnd(), bedFeature.getEnd());
        assertEquals(gffFeature.getStrand(), bedFeature.getStrand());
        assertEquals(gffFeature.getColor(), bedFeature.getColor());
        //BED features don't have a type
        //assertEquals(gffFeature.getType(), bedFeature.getType());
        assertEquals(gffFeature.getThickStart(), bedFeature.getThickStart());
        assertEquals(gffFeature.getThickEnd(), bedFeature.getThickEnd());
        if (!Float.isNaN(gffFeature.getScore())) {
            assertEquals(gffFeature.getScore(), bedFeature.getScore());
        }
        assertEquals(gffFeature.getExonCount(), bedFeature.getExonCount());

        List<Exon> gffExons = gffFeature.getExons();
        List<Exon> bedExons = bedFeature.getExons();

        // This is broken for sure, disable for now
//        for (int i = 0; i < gffExons.size(); i++) {
//
//            Exon gffExon = gffExons.get(i);
//            Exon bedExon = bedExons.get(i);
//            assertEquals(gffExon.getCdStart(), bedExon.getCdStart());
//            assertEquals(gffExon.getCodingLength(), bedExon.getCodingLength());
//            assertEquals(gffExon.getCdEnd(), bedExon.getCdEnd());
//            assertEquals(gffExon.getReadingShift(), bedExon.getReadingShift());
//        }

    }
}
