/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 Broad Institute
 *
 * 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.broad.igv.variant.vcf;

import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.track.FeatureSource;
import org.broad.igv.track.TribbleFeatureSource;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.Feature;
import htsjdk.tribble.readers.PositionalBufferedStream;
import htsjdk.variant.bcf2.BCF2Codec;
import org.junit.Ignore;
import org.junit.Test;

import java.io.FileInputStream;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

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

/**
 * @author jacob
 * @date 2013-Jun-14
 */
public class BCFReaderTest extends AbstractHeadlessTest {


    /**
     * Just test that we load a BCF file without crashing
     *
     * @throws Exception
     */
    @Test
    public void loadBCF() throws Exception {
        String path = TestUtils.DATA_DIR + "bcf/ex2.bcf";
        FeatureSource source = TribbleFeatureSource.getFeatureSource(new ResourceLocator(path), genome);
        Iterator<Feature> features = source.getFeatures("chr20", 14000, 1300000);
        int count = 0;

        while (features.hasNext()) {
            features.next();
            count++;
        }

        assertTrue("No features read", count > 0);
    }

    /**
     * Compare a BCF and VCF file
     *
     * @throws Exception
     */
    @Test
    public void compareBCFtoVCF() throws Exception {
        String BCF2path = TestUtils.DATA_DIR + "bcf/ex2.bcf";
        FeatureSource BCF2source = TribbleFeatureSource.getFeatureSource(new ResourceLocator(BCF2path), genome);
        Iterator<Feature> BCF2features = BCF2source.getFeatures("chr20", 14000, 1300000);
        List<VCFVariant> BCF2List = new ArrayList<VCFVariant>();

        String VCFpath = TestUtils.DATA_DIR + "vcf/ex2.vcf";
        TestUtils.createIndex(VCFpath);
        FeatureSource VCFsource = TribbleFeatureSource.getFeatureSource(new ResourceLocator(VCFpath), genome);
        Iterator<Feature> VCFfeatures = VCFsource.getFeatures("chr20", 14000, 1300000);
        List<VCFVariant> VCFList = new ArrayList<VCFVariant>();

        while (BCF2features.hasNext()) {
            VCFVariant bcfV = (VCFVariant) BCF2features.next();
            VCFVariant vcfV = (VCFVariant) VCFfeatures.next();

            assertEquals(vcfV.getType(), bcfV.getType());

            BCF2List.add(bcfV);
            VCFList.add(vcfV);
        }

        TestUtils.assertFeatureListsEqual(VCFList.iterator(), BCF2List.iterator());
    }

    //Quick method for checking if a bcf file has the magic header
    @Ignore
    //@Test
    public void rawTestFile() throws Exception {
        String path = "/path/to/myfile.bcf";
        PositionalBufferedStream ps = new PositionalBufferedStream(new FileInputStream(path));

        BCF2Codec codec = new BCF2Codec();
        codec.readHeader(ps);

    }


}