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

import htsjdk.samtools.reference.ReferenceSequenceFile;
import htsjdk.variant.variantcontext.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.List;
import java.util.HashMap;
import java.util.Map;

import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.Test;

class AlwaysTrueMergeRule extends PhasingUtils.AlleleMergeRule {
    public boolean allelesShouldBeMerged(VariantContext vc1, VariantContext vc2) {
        return true;
    }
}

public class PhasingUtilsUnitTest extends BaseTest {

    private final int start = 10;
    GenomeLocParser genomeLocParser;
    private ReferenceSequenceFile referenceFile;
    private Genotype genotype1;
    private Genotype genotype2;
    private Genotype genotype2unphased;
    private String contig;
    private List<Allele> alleleList1;
    private List<Allele> alleleList2;
    VariantContext vc1;
    VariantContext vc2;

    @BeforeSuite
    public void init() throws FileNotFoundException {
        referenceFile = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(referenceFile);
        alleleList1 = Arrays.asList(Allele.create("T", true), Allele.create("C", false));
        alleleList2 = Arrays.asList(Allele.create("G", true), Allele.create("A", false));
        genotype1 = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).attribute("PQ", 100.0).alleles(alleleList1).phased(true).make();
        genotype2 = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-2", "10-1"}).attribute("PQ", 200.0).alleles(alleleList2).phased(true).make();
        genotype2unphased = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-2", "10-1"}).attribute("PQ", 200.0).alleles(alleleList2).phased(false).make();
        contig = new String("1");
        vc1 = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(genotype1).make();
        vc2 = new VariantContextBuilder().chr(contig).id("id2").source("GA").start(start+1).stop(start+1).alleles(alleleList2).genotypes(genotype2).make();
    }

    @Test
    public void TestMatchHaplotypeAllelesKeyHP() {

        final PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(genotype1, genotype2);

        final PhasingUtils.SameHaplotypeAlleles sameHaplotypeAllelesExpected = new PhasingUtils.SameHaplotypeAlleles();
        sameHaplotypeAllelesExpected.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("T", true), Allele.create("A", false)));
        sameHaplotypeAllelesExpected.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("C", false), Allele.create("G", true)));
        sameHaplotypeAllelesExpected.requiresSwap = true;

        Assert.assertEquals(sameHaplotypeAlleles.hapAlleles, sameHaplotypeAllelesExpected.hapAlleles);
        Assert.assertEquals(sameHaplotypeAlleles.requiresSwap, sameHaplotypeAllelesExpected.requiresSwap);
    }

    @Test
    public void TestMatchHaplotypeAllelesNoKeyHP() {

        final Genotype genotypeNoKeyHP1 = new GenotypeBuilder().name("TC").alleles(alleleList1).make();
        final Genotype genotypeNoKeyHP2 = new GenotypeBuilder().name("GA").alleles(alleleList2).make();

        final PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(genotypeNoKeyHP1, genotypeNoKeyHP2);
        final PhasingUtils.SameHaplotypeAlleles sameHaplotypeAllelesExpected = new PhasingUtils.SameHaplotypeAlleles();
        sameHaplotypeAllelesExpected.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("T", true), Allele.create("G", true)));
        sameHaplotypeAllelesExpected.hapAlleles.add(new PhasingUtils.AlleleOneAndTwo(Allele.create("C", false), Allele.create("A", false)));
        Assert.assertEquals(sameHaplotypeAlleles.hapAlleles, sameHaplotypeAllelesExpected.hapAlleles);
        Assert.assertEquals(sameHaplotypeAlleles.requiresSwap, sameHaplotypeAllelesExpected.requiresSwap);
    }

    @Test
    public void TestMergeIntoMNPvalidationTrueCheck() {
        Assert.assertTrue(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc1, vc2));
    }

    @Test
    public void TestMergeIntoMNPvalidationCheckLocBefore() {
        final VariantContext vc1before = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start+1).stop(start+1).alleles(alleleList1).make();
        final VariantContext vc2after = new VariantContextBuilder().chr(contig).id("id2").source("GA").start(start).stop(start).alleles(alleleList2).make();
        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc1before, vc2after));
    }

    @Test
    public void TestMergeIntoMNPvalidationFiltered() {
        final List<String> filters = Arrays.asList("filter");
        final Genotype genotype = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList1).filters(filters).make();
        final VariantContext vc = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(genotype).make();
        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc, vc2));
    }

    @Test
    public void TestMergeIntoMNPvalidationFilterNoCall() {
        final List<String> filters = Arrays.asList("filter");
        final List<Allele> alleleList = Arrays.asList(Allele.create("T", true), Allele.create(".", false));
        final Genotype genotype = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList).filters(filters).make();
        final VariantContext vc = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(genotype).make();
        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc, vc2));
    }

    @Test
    public void TestMergeIntoMNPvalidationDiffSampleNames() {
        final Genotype genotype = new GenotypeBuilder().name("sample1").attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList1).make();
        final VariantContext vc = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(genotype).make();
        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc, vc2));
    }

    @Test
    public void TestMergeIntoMNPvalidationDiffContigs() {
        final String contig = new String("2");
        final VariantContext vc = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start+1).stop(start+1).alleles(alleleList2).genotypes(genotype2).make();
        Assert.assertFalse(PhasingUtils.mergeIntoMNPvalidationCheck(genomeLocParser, vc1, vc));
    }

    @Test
    public void TestMergeVariantContextAttributes() {
        Assert.assertEquals(0, PhasingUtils.mergeVariantContextAttributes(vc1, vc2).size());
    }

    @Test
    public void TestAllSamplesAreMergeable() {
        Assert.assertTrue(PhasingUtils.allSamplesAreMergeable(vc1, vc2));
    }

    @Test
    public void TestAlleleSegregationIsKnown(){
        Assert.assertTrue(PhasingUtils.alleleSegregationIsKnown(genotype1, genotype2));
        Assert.assertFalse(PhasingUtils.alleleSegregationIsKnown(genotype1, genotype2unphased));
    }

    @Test
    public void TestSomeSampleHasDoubleNonReferenceAlleleTrue(){
        Genotype genotype = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList2).make();
        VariantContext vc = new VariantContextBuilder().chr(contig).id("id2").source("GA").start(start+1).stop(start+1).alleles(alleleList2).genotypes(genotype).make();
        Assert.assertTrue(PhasingUtils.someSampleHasDoubleNonReferenceAllele(vc1, vc));
    }

    @Test
    public void TestSomeSampleHasDoubleNonReferenceAlleleFalse(){
        Assert.assertFalse(PhasingUtils.someSampleHasDoubleNonReferenceAllele(vc1, vc2));
    }

    @Test
    public void TestDoubleAllelesSegregatePerfectlyAmongSamples(){
        final Genotype genotype = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).alleles(alleleList2).make();
        final VariantContext vc = new VariantContextBuilder().chr(contig).id("id2").source("GA").start(start+1).stop(start+1).alleles(alleleList2).genotypes(genotype).make();
        Assert.assertTrue(PhasingUtils.doubleAllelesSegregatePerfectlyAmongSamples(vc1, vc));
    }

    @Test
    public void TestMergeVariantContextNames() {
        final String result = new String("A_B");
        Assert.assertEquals(result, PhasingUtils.mergeVariantContextNames("A", "B"));
    }

    @Test
    public void TestMergeIntoMNP(){
        final AlwaysTrueMergeRule alleleMergeRule = new AlwaysTrueMergeRule();
        final VariantContext vc = PhasingUtils.mergeIntoMNP(genomeLocParser, vc1, vc2, referenceFile, alleleMergeRule);

        final List<Allele> alleleList = Arrays.asList(Allele.create("TG", true), Allele.create("TA", false), Allele.create("CG", false));
        final Map<String,Object> attributes = new HashMap<String,Object>(){{
            put("AC", new ArrayList<Integer>(Arrays.asList(1, 1)));
            put("AF", new ArrayList<Double>(Arrays.asList(0.5, 0.5)));
            put("AN", 2);
        }};
        final Map<String, Object> extendedAttributes = new HashMap<String, Object>(){{
            put("PQ", 100.0); put("HP", new String[]{"10-1", "10-2"});
        }};
        final List<Allele> alleleListMeged = Arrays.asList(Allele.create("TA"), Allele.create("CG"));
        final Genotype genotype = new GenotypeBuilder().name("sample").attributes(extendedAttributes).alleles(alleleListMeged).make();
        final VariantContext vcExpected = new VariantContextBuilder().chr(contig).id("id1;id2").source("TC_GA").start(start).stop(start+1).alleles(alleleList).genotypes(genotype).attributes(attributes).make();
        Assert.assertTrue(genotype.sameGenotype(vcExpected.getGenotypes().get("sample")));
        Assert.assertTrue(vcExpected.hasSameAllelesAs(vc));
        Assert.assertEquals(vcExpected.getChr(), vc.getChr());
        Assert.assertEquals(vcExpected.getStart(), vc.getStart());
        Assert.assertEquals(vcExpected.getEnd(), vc.getEnd());
        Assert.assertEquals(vcExpected.getID(), vc.getID());
        Assert.assertEquals(vcExpected.getSource(), vc.getSource());
        Assert.assertEquals(vcExpected.isFiltered(), vc.isFiltered());
        Assert.assertEquals(vcExpected.getPhredScaledQual(), vc.getPhredScaledQual());
        Assert.assertEquals(vcExpected.getAttribute("PQ"), vc.getAttribute("PQ"));
        Assert.assertEquals(vcExpected.getAttribute("HP"), vc.getAttribute("HP"));
    }

    @Test
    public void TestReallyMergeIntoMNP( ){
        final VariantContext vc = PhasingUtils.reallyMergeIntoMNP(vc1, vc2, referenceFile);

        final List<Allele> alleleList = Arrays.asList(Allele.create("TG", true), Allele.create("TA", false), Allele.create("CG", false));
        final Map<String,Object> attributes = new HashMap<String,Object>(){{
            put("AC", new ArrayList<Integer>(Arrays.asList(1, 1)));
            put("AF", new ArrayList<Double>(Arrays.asList(0.5, 0.5)));
            put("AN", 2);
        }};
        final Map<String, Object> extendedAttributes = new HashMap<String, Object>(){{
            put("PQ", 100.0); put("HP", new String[]{"10-1", "10-2"});
        }};
        final List<Allele> alleleListMeged = Arrays.asList(Allele.create("TA"), Allele.create("CG"));
        final Genotype genotype = new GenotypeBuilder().name("sample").attributes(extendedAttributes).alleles(alleleListMeged).make();
        final VariantContext vcExpected = new VariantContextBuilder().chr(contig).id("id1;id2").source("TC_GA").start(start).stop(start+1).alleles(alleleList).genotypes(genotype).attributes(attributes).make();
        Assert.assertTrue(genotype.sameGenotype(vcExpected.getGenotypes().get("sample")));
        Assert.assertTrue(vcExpected.hasSameAllelesAs(vc));
        Assert.assertEquals(vcExpected.getChr(), vc.getChr());
        Assert.assertEquals(vcExpected.getStart(), vc.getStart());
        Assert.assertEquals(vcExpected.getEnd(), vc.getEnd());
        Assert.assertEquals(vcExpected.getID(), vc.getID());
        Assert.assertEquals(vcExpected.getSource(), vc.getSource());
        Assert.assertEquals(vcExpected.isFiltered(), vc.isFiltered());
        Assert.assertEquals(vcExpected.getPhredScaledQual(), vc.getPhredScaledQual());
        Assert.assertEquals(vcExpected.getAttribute("PQ"), vc.getAttribute("PQ"));
        Assert.assertEquals(vcExpected.getAttribute("HP"), vc.getAttribute("HP"));
    }

    @Test
    public void TestAllGenotypesAreUnfilteredAndCalled(){
        final VariantContext vc = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(genotype1).make();
        Assert.assertTrue(PhasingUtils.allGenotypesAreUnfilteredAndCalled(vc));
    }

    @Test
    public void TestEnsureMergedAllele(){
        byte[] intermediateBases = new byte[]{'A','T'};
        final PhasingUtils.MergedAllelesData mergeData = new PhasingUtils.MergedAllelesData(intermediateBases, vc1, vc2);
        final Allele allele = mergeData.ensureMergedAllele(Allele.create("T", true), Allele.create("C", true));
        final Allele expectedAllele = Allele.create(new byte[]{'T', 'A', 'T', 'C'}, false);
        Assert.assertEquals(allele, expectedAllele);
    }

}
