/*
* 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.engine.filters;

import htsjdk.samtools.Cigar;
import org.broadinstitute.gatk.utils.sam.CigarUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

/**
 * @author ami
 * @since 04/22/14
 */
public class NDNCigarReadTransformerUnitTest {


    @DataProvider(name = "filteringIteratorTestData")
    public String[][] getFilteringIteratorTestData() {
        return new String[][] {
                {"1M1N1N1M","1M1N1N1M"},           // NN elements
                {"1M1N1D4M","1M1N1D4M"},           // ND
                {"1M1N3M","1M1N3M"},               // N
                {"1M1N2I1N3M","1M1N2I1N3M"},       // NIN
                {"1M1N3D2N1M","1M6N1M"},
                {"1M2N2D2N1M1D3N1D1N1M2H","1M6N1M1D5N1M2H"},
                {"1H2S1M1N3D2N1M","1H2S1M6N1M"},
                {"10M628N2D203N90M","10M833N90M"}
        };
    }

    NDNCigarReadTransformer filter;

    @BeforeClass
    public void init() {
        filter = new NDNCigarReadTransformer();
    }

    @Test(dataProvider = "filteringIteratorTestData")
    public void testCigarRefactoring (final String originalCigarString, final String expectedString) {
        Cigar originalCigar = CigarUtils.cigarFromString(originalCigarString);
        String actualString = filter.refactorNDNtoN(originalCigar).toString();
        Assert.assertEquals(actualString, expectedString, "ciagr string "+ originalCigarString+" should become: "+expectedString+" but got: "+actualString);
    }

}
