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package org.broadinstitute.gatk.tools.walkers.variantutils;

import htsjdk.variant.variantcontext.*;
import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Tests {@link org.broadinstitute.gatk.tools.walkers.variantutils.ReferenceConfidenceVariantContextMerger}.
 *
 * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
 */
public class VariantContextMergerUnitTest  extends BaseTest {
    Allele Aref, T, C, G, Cref, ATC, ATCATC;
    Allele ATCATCT;
    Allele ATref;
    Allele Anoref;
    Allele GT;
    Allele del;

    private GenomeLocParser genomeLocParser;

    @BeforeSuite
    public void setup() throws IOException {
        // alleles
        Aref = Allele.create("A", true);
        Cref = Allele.create("C", true);
        T = Allele.create("T");
        C = Allele.create("C");
        G = Allele.create("G");
        ATC = Allele.create("ATC");
        ATCATC = Allele.create("ATCATC");
        ATCATCT = Allele.create("ATCATCT");
        ATref = Allele.create("AT",true);
        Anoref = Allele.create("A",false);
        del = Allele.SPAN_DEL;
        GT = Allele.create("GT",false);
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(hg18Reference)));
    }

    @Test(dataProvider = "referenceConfidenceMergeData")
    public void testReferenceConfidenceMerge(final String testID, final List<VariantContext> toMerge, final GenomeLoc loc,
                                             final boolean returnSiteEvenIfMonomorphic, final boolean uniquifySamples, final VariantContext expectedResult) {
        final VariantContext result = ReferenceConfidenceVariantContextMerger.merge(toMerge, loc, returnSiteEvenIfMonomorphic ? (byte) 'A' : null, true, uniquifySamples);
        if ( result == null ) {
            Assert.assertTrue(expectedResult == null);
            return;
        }
        Assert.assertEquals(result.getAlleles(), expectedResult.getAlleles(),testID);
        Assert.assertEquals(result.getNSamples(), expectedResult.getNSamples(),testID);
        for ( final Genotype expectedGenotype : expectedResult.getGenotypes() ) {
            Assert.assertTrue(result.hasGenotype(expectedGenotype.getSampleName()), "Missing " + expectedGenotype.getSampleName());
            // use string comparisons to test equality for now
            Assert.assertEquals(result.getGenotype(expectedGenotype.getSampleName()).toString(), expectedGenotype.toString());
        }
    }

    @Test
    public void testGenerateADWithNewAlleles() {

        final int[] originalAD = new int[] {1,2,0};
        final int[] indexesOfRelevantAlleles = new int[] {0,1,2,2};

        final int[] newAD = ReferenceConfidenceVariantContextMerger.generateAD(originalAD, indexesOfRelevantAlleles);
        Assert.assertEquals(newAD, new int[]{1,2,0,0});
    }


    @Test(expectedExceptions = UserException.class)
    public void testGetIndexesOfRelevantAllelesWithNoALT() {

        final List<Allele> alleles1 = new ArrayList<>(1);
        alleles1.add(Allele.create("A", true));
        final List<Allele> alleles2 = new ArrayList<>(1);
        alleles2.add(Allele.create("A", true));
        GenotypeBuilder builder = new GenotypeBuilder();
        ReferenceConfidenceVariantContextMerger.getIndexesOfRelevantAlleles(alleles1, alleles2, -1, builder.make());
        Assert.fail("We should have thrown an exception because the <ALT> allele was not present");
    }

    @Test(dataProvider = "getIndexesOfRelevantAllelesData")
    public void testGetIndexesOfRelevantAlleles(final int allelesIndex, final List<Allele> allAlleles) {
        final List<Allele> myAlleles = new ArrayList<>(3);

        // always add the reference and <ALT> alleles
        myAlleles.add(allAlleles.get(0));
        myAlleles.add(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        // optionally add another alternate allele
        if ( allelesIndex > 0 )
            myAlleles.add(allAlleles.get(allelesIndex));

        GenotypeBuilder builder = new GenotypeBuilder();

        final int[] indexes = ReferenceConfidenceVariantContextMerger.getIndexesOfRelevantAlleles(myAlleles, allAlleles, -1, builder.make());

        Assert.assertEquals(indexes.length, allAlleles.size());

        for ( int i = 0; i < allAlleles.size(); i++ ) {
            if ( i == 0 )
                Assert.assertEquals(indexes[i], 0);    // ref should always match
            else if ( i == allelesIndex )
                Assert.assertEquals(indexes[i], 2);    // allele
            else
                Assert.assertEquals(indexes[i], 1);    // <ALT>
        }
    }


    @DataProvider(name = "referenceConfidenceMergeData")
    public Object[][] makeReferenceConfidenceMergeData() {
        final List<Object[]> tests = new ArrayList<>();
        final int start = 10;
        final GenomeLoc loc = new UnvalidatingGenomeLoc("20", 0, start, start);
        final VariantContext VCbase = new VariantContextBuilder("test", "20", start, start, Arrays.asList(Aref)).make();
        final VariantContext VCbase2 = new VariantContextBuilder("test2", "20", start, start, Arrays.asList(Aref)).make();
        final VariantContext VCprevBase = new VariantContextBuilder("test", "20", start-1, start-1, Arrays.asList(Aref)).make();

        final int[] standardPLs = new int[]{30, 20, 10, 71, 72, 73};
        final int[] reorderedSecondAllelePLs = new int[]{30, 71, 73, 20, 72, 10};

        final List<Allele> noCalls = new ArrayList<>(2);
        noCalls.add(Allele.NO_CALL);
        noCalls.add(Allele.NO_CALL);

        final List<Allele> A_ALT = Arrays.asList(Aref, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gA_ALT = new GenotypeBuilder("A").PL(new int[]{0, 100, 1000}).alleles(noCalls).make();
        final VariantContext vcA_ALT = new VariantContextBuilder(VCbase).alleles(A_ALT).genotypes(gA_ALT).make();

        final Allele AAref = Allele.create("AA", true);
        final List<Allele> AA_ALT = Arrays.asList(AAref, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gAA_ALT = new GenotypeBuilder("AA").PL(new int[]{0, 80, 800}).alleles(noCalls).make();
        final VariantContext vcAA_ALT = new VariantContextBuilder(VCprevBase).alleles(AA_ALT).genotypes(gAA_ALT).make();

        final List<Allele> A_C = Arrays.asList(Aref, C);
        final Genotype gA_C = new GenotypeBuilder("A_C").PL(new int[]{30, 20, 10}).alleles(noCalls).make();
        final List<Allele> A_C_ALT = Arrays.asList(Aref, C, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gA_C_ALT = new GenotypeBuilder("A_C").PL(standardPLs).alleles(noCalls).make();
        final VariantContext vcA_C = new VariantContextBuilder(VCbase2).alleles(A_C_ALT).genotypes(gA_C).make();
        final VariantContext vcA_C_ALT = new VariantContextBuilder(VCbase).alleles(A_C_ALT).genotypes(gA_C_ALT).make();

        final List<Allele> A_G_ALT = Arrays.asList(Aref, G, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gA_G_ALT = new GenotypeBuilder("A_G").PL(standardPLs).alleles(noCalls).make();
        final VariantContext vcA_G_ALT = new VariantContextBuilder(VCbase).alleles(A_G_ALT).genotypes(gA_G_ALT).make();

        final List<Allele> A_C_G = Arrays.asList(Aref, C, G);
        final Genotype gA_C_G = new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30}).alleles(noCalls).make();
        final List<Allele> A_C_G_ALT = Arrays.asList(Aref, C, G, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gA_C_G_ALT = new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30, 71, 72, 73, 74}).alleles(noCalls).make();
        final VariantContext vcA_C_G = new VariantContextBuilder(VCbase2).alleles(A_C_G_ALT).genotypes(gA_C_G).make();
        final VariantContext vcA_C_G_ALT = new VariantContextBuilder(VCbase).alleles(A_C_G_ALT).genotypes(gA_C_G_ALT).make();

        final List<Allele> A_ATC_ALT = Arrays.asList(Aref, ATC, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gA_ATC_ALT = new GenotypeBuilder("A_ATC").PL(standardPLs).alleles(noCalls).make();
        final VariantContext vcA_ATC_ALT = new VariantContextBuilder(VCbase).alleles(A_ATC_ALT).genotypes(gA_ATC_ALT).make();

        final Allele A = Allele.create("A", false);
        final List<Allele> AA_A_ALT = Arrays.asList(AAref, A, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
        final Genotype gAA_A_ALT = new GenotypeBuilder("AA_A").PL(standardPLs).alleles(noCalls).make();
        final VariantContext vcAA_A_ALT = new VariantContextBuilder(VCprevBase).alleles(AA_A_ALT).genotypes(gAA_A_ALT).make();
        final List<Allele> A_C_del = Arrays.asList(Aref, C, del);

        // first test the case of a single record
        tests.add(new Object[]{"test00",Arrays.asList(vcA_C_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(A_C).genotypes(gA_C).make()});

        // now, test pairs:
        // a SNP with another SNP
        tests.add(new Object[]{"test01",Arrays.asList(vcA_C_ALT, vcA_G_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(A_C_G).genotypes(gA_C_ALT, new GenotypeBuilder("A_G").PL(reorderedSecondAllelePLs).alleles(noCalls).make()).make()});
        // a SNP with an indel
        tests.add(new Object[]{"test02",Arrays.asList(vcA_C_ALT, vcA_ATC_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(Arrays.asList(Aref, C, ATC)).genotypes(gA_C_ALT, new GenotypeBuilder("A_ATC").PL(reorderedSecondAllelePLs).alleles(noCalls).make()).make()});
        // a SNP with 2 SNPs
        tests.add(new Object[]{"test03",Arrays.asList(vcA_C_ALT, vcA_C_G_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(A_C_G).genotypes(gA_C_ALT, gA_C_G).make()});
        // a SNP with a ref record
        tests.add(new Object[]{"test04",Arrays.asList(vcA_C_ALT, vcA_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(A_C).genotypes(gA_C, gA_ALT).make()});

        // spanning records:
        // a SNP with a spanning ref record
        tests.add(new Object[]{"test05",Arrays.asList(vcA_C_ALT, vcAA_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(A_C).genotypes(gA_C, gAA_ALT).make()});
        // a SNP with a spanning deletion
        tests.add(new Object[]{"test06",Arrays.asList(vcA_C_ALT, vcAA_A_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(A_C_del).genotypes(new GenotypeBuilder("A_C").PL(new int[]{30, 20, 10, 71, 72, 73}).alleles(noCalls).make(),
                        new GenotypeBuilder("AA_A").PL(new int[]{30, 71, 73, 20, 72, 10}).alleles(noCalls).make()).make()});

        // combination of all
        tests.add(new Object[]{"test07",Arrays.asList(vcA_C_ALT, vcA_G_ALT, vcA_ATC_ALT, vcA_C_G_ALT, vcA_ALT, vcAA_ALT, vcAA_A_ALT),
                loc, false, false,
                new VariantContextBuilder(VCbase).alleles(Arrays.asList(Aref, C, G, ATC, del)).genotypes(new GenotypeBuilder("A_C").PL(new int[]{30, 20, 10, 71, 72, 73, 71, 72, 73, 73, 71, 72, 73, 73, 73}).alleles(noCalls).make(),
                        new GenotypeBuilder("A_G").PL(new int[]{30, 71, 73, 20, 72, 10, 71, 73, 72, 73, 71, 73, 72, 73, 73}).alleles(noCalls).make(),
                        new GenotypeBuilder("A_ATC").PL(new int[]{30, 71, 73, 71, 73, 73, 20, 72, 72, 10, 71, 73, 73, 72, 73}).alleles(noCalls).make(),
                        new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30, 71, 72, 73, 74, 71, 72, 73, 74, 74}).alleles(noCalls).make(),
                        new GenotypeBuilder("A").PL(new int[]{0, 100, 1000, 100, 1000, 1000, 100, 1000, 1000, 1000, 100, 1000, 1000, 1000, 1000}).alleles(noCalls).make(),
                        new GenotypeBuilder("AA").PL(new int[]{0, 80, 800, 80, 800, 800, 80, 800, 800, 800, 80, 800, 800, 800, 800}).alleles(noCalls).make(),
                        new GenotypeBuilder("AA_A").PL(new int[]{30, 71, 73, 71, 73, 73, 71, 73, 73, 73, 20, 72, 72, 72, 10}).alleles(noCalls).make()).make()});

        // just spanning ref contexts, trying both instances where we want/do not want ref-only contexts
        tests.add(new Object[]{"test08",Arrays.asList(vcAA_ALT),

                loc, false, false,
                null});
        tests.add(new Object[]{"test09", Arrays.asList(vcAA_ALT),
                loc, true, false,
                new VariantContextBuilder(VCbase).alleles(Arrays.asList(Allele.create("A", true))).genotypes(new GenotypeBuilder("AA").PL(new int[]{0}).alleles(noCalls).make()).make()});

        // test uniquification of sample names
        tests.add(new Object[]{"test10",Arrays.asList(vcA_C, vcA_C_ALT), loc, false, true,
                new VariantContextBuilder(VCbase).alleles(A_C).genotypes(
                        new GenotypeBuilder("A_C.test2").PL(new int[]{30, 20, 10}).alleles(noCalls).make(),
                        new GenotypeBuilder("A_C.test").PL(new int[]{30, 20, 10}).alleles(noCalls).make()).make()});

        tests.add(new Object[]{"test11",Arrays.asList(vcA_C_G, vcA_C_G_ALT), loc, false, true,
                new VariantContextBuilder(VCbase).alleles(A_C_G).genotypes(
                        new GenotypeBuilder("A_C_G.test2").PL(new int[]{40, 20, 30, 20, 10, 30}).alleles(noCalls).make(),
                        new GenotypeBuilder("A_C_G.test").PL(new int[]{40, 20, 30, 20, 10, 30}).alleles(noCalls).make()).make()});

        final Object[][] result = tests.toArray(new Object[][]{});
        return result;
    }
    @DataProvider(name = "getIndexesOfRelevantAllelesData")
    public Object[][] makeGetIndexesOfRelevantAllelesData() {
        final int totalAlleles = 5;
        final List<Allele> alleles = new ArrayList<>(totalAlleles);
        alleles.add(Allele.create("A", true));
        for ( int i = 1; i < totalAlleles; i++ )
            alleles.add(Allele.create(Utils.dupString('A', i + 1), false));

        final List<Object[]> tests = new ArrayList<>();

        for ( int alleleIndex = 0; alleleIndex < totalAlleles; alleleIndex++ ) {
            tests.add(new Object[]{alleleIndex, alleles});
        }

        return tests.toArray(new Object[][]{});
    }
}
