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

import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;

import java.util.Arrays;

public class SymbolicAllelesIntegrationTest extends WalkerTest {

    public static String baseTestString(String reference, String VCF) {
        return "-T CombineVariants" +
                " -R " + reference +
                " --variant:vcf " + validationDataLocation + VCF +
                " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
                " -genotypeMergeOptions REQUIRE_UNIQUE" +
                " -setKey null" +
                " -o %s" +
                " -NO_HEADER";
    }


    @Test
    public void test1() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
                1,
                Arrays.asList("89a1c56f264ac27a2a4be81072473b6f"));
        executeTest("Test symbolic alleles", spec);
    }

    @Test
    public void test2() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                1,
                Arrays.asList("3008d6f5044bc14801e5c58d985dec72"));
        executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
    }
}

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

import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;

import java.util.Arrays;

public class SymbolicAllelesIntegrationTest extends WalkerTest {

    public static String baseTestString(String reference, String VCF) {
        return "-T CombineVariants" +
                " -R " + reference +
                " --variant:vcf " + validationDataLocation + VCF +
                " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
                " -genotypeMergeOptions REQUIRE_UNIQUE" +
                " -setKey null" +
                " -o %s" +
                " -NO_HEADER";
    }


    @Test
    public void test1() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
                1,
                Arrays.asList("89a1c56f264ac27a2a4be81072473b6f"));
        executeTest("Test symbolic alleles", spec);
    }

    @Test
    public void test2() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                1,
                Arrays.asList("6645babc8c7d46be0da223477c7b1291"));
        executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
    }
}

Revert "Updating md5 for fixed file" because this was fixed properly in unstable (but will break SnpEff if put into Stable).
Revert "Updating md5 for fixed file" because this was fixed properly in unstable (but will break SnpEff if put into Stable).

This reverts commit 6b4182c6ab3e214da4c73bc6f3687ac6d1c0b72c.
