package org.broadinstitute.sting.gatk.walkers.sequenom;

import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;

import java.util.Arrays;

public class SequenomValidationConverterIntegrationTest extends WalkerTest {

    public void testEmpty() {
        System.err.println("Reinstate these tests when plink is back in");
    }

    //@Test TODO: reinstate the test when the Plink rod is back
    public void testSNPs() {
        String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                Arrays.asList("2dab4630f40b76c0762de83fcbb60d09"));
        executeTest("Test SNPs", spec);
    }

//    @Test
    // TODO- need to be reenabled when PED reader tracks gets updated to read indels correctly
    public void testIndels() {
        String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                Arrays.asList("fad2dd71550dec064d458c4aa83e4de9"));
        executeTest("Test Indels", spec);
    }
}
