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

import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.PositionalBufferedStream;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCodec;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.testng.Assert;
import org.testng.annotations.Test;

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

public class GenotypeGVCFsIntegrationTest extends WalkerTest {

    private static String baseTestString(String args, String ref) {
        return "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + ref + args;
    }

    private static String baseBPResolutionString(String args) {
        return baseTestString(" -V " + privateTestDir + "gvcf.basepairResolution.vcf " + args, b37KGReference);
    }

    @Test(enabled = true)
    public void testUpdatePGT() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
                1,
                Arrays.asList("9424ae7832fd53790372578423392468"));
        executeTest("testUpdatePGT", spec);
    }

    @Test(enabled = true)
    public void testUpdatePGTStrandAlleleCountsBySample() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample", b37KGReference),
                1,
                Arrays.asList("5deed67f8eb10cbd4429d70e0c26ef7c"));
        executeTest("testUpdatePGT, adding StrandAlleleCountsBySample annotation", spec);
    }

    @Test(enabled = true)
    public void combineSingleSamplePipelineGVCF() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
                        " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                        " -L 20:10,000,000-20,000,000", b37KGReference),
                1,
                Arrays.asList("6df12487566b55c4cdbc0993ddf4a75e"));
        executeTest("combineSingleSamplePipelineGVCF", spec);
    }

    @Test(enabled = true)
    public void testTetraploidRun() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:sample1 " + privateTestDir + "tetraploid-gvcf-1.vcf" +
                        " -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" +
                        " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                        " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                1,
                Arrays.asList("e0a51868271fb7b399478b9c63ede291"));
        executeTest("combineSingleSamplePipelineGVCF", spec);
    }

    @Test(enabled= true)
    public void testMixedPloidyRun() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:sample1 " + privateTestDir + "haploid-gvcf-1.vcf" +
                        " -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" +
                        " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                        " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                1,
                Arrays.asList("1e4be55f727c7a9376a7a37406f06cee"));
        executeTest("combineSingleSamplePipelineGVCF", spec);
    }

    @Test(enabled = true)
    public void combineSingleSamplePipelineGVCF_includeNonVariants() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
                        " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                        " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
                1,
                Arrays.asList("92513f9a6f34829ef455a379e87e09cd"));
        executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
    }

    @Test(enabled = true)
    public void combineSingleSamplePipelineGVCFHierarchical() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                        " -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
                        " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                        " -L 20:10,000,000-20,000,000", b37KGReference),
                1,
                Arrays.asList("95e21516ef7a71de9b299d502e83268e"));
        executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
    }

    @Test(enabled = true)
    public void combineSingleSamplePipelineGVCF_addDbsnp() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
                        " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                        " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
                1,
                Arrays.asList("f352d0204a37a7adc4000318d5f24cb8"));
        executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
    }

    @Test(enabled = true)
    public void testJustOneSample() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
                " -V " + privateTestDir + "gvcfExample1.vcf",
                1,
                Arrays.asList("88ef27a16fc44a3caa700677d5b78df5"));
        executeTest("testJustOneSample", spec);
    }

    @Test(enabled = true)
    public void testSamplesWithDifferentLs() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "gvcfExample1.vcf" +
                        " -V " + privateTestDir + "gvcfExample2.vcf",
                1,
                Arrays.asList("45d9c291a74897cf3c3aaf52af5a08f8"));
        executeTest("testSamplesWithDifferentLs", spec);
    }

    @Test(enabled = true)
    public void testNoPLsException() {
        // Test with input files with (1) 0/0 and (2) ./.
        final String md5 = "2dd285987047f37c730060734ca76038";
        WalkerTestSpec spec1 = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
                        " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
                1,
                Arrays.asList(md5));
        WalkerTestSpec spec2 = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
                        " --variant " + privateTestDir + "combined_genotype_gvcf_exception.nocall.vcf",
                1,
                Arrays.asList(md5));
        executeTest("testNoPLsException.1", spec1);
        executeTest("testNoPLsException.2", spec2);
    }

    @Test
    public void testNDA() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseBPResolutionString("-nda"),
                1,
                Arrays.asList("b7fda2981a2367764b83df7aa3b3b3e7"));
        executeTest("testNDA", spec);
    }

    @Test
    public void testMaxAltAlleles() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseBPResolutionString("-maxAltAlleles 1"),
                1,
                Arrays.asList("0c26cabfcebfb0b662185b233e0cd976"));
        executeTest("testMaxAltAlleles", spec);
    }

    @Test
    public void testStandardConf() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
                1,
                Arrays.asList("102c33e8b2a7200972d58fc6bae8bd3b"));
        executeTest("testStandardConf", spec);
    }

    @Test
    public void testStrandAlleleCountsBySample() throws IOException {
        //HaplotypeCaller creates gVCF
        final String CEUTRIO_BAM = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
        final WalkerTestSpec specHaplotypeCaller = new WalkerTestSpec(
                "-T HaplotypeCaller --disableDithering " +
                        String.format("-R %s -I %s ", b37KGReference, CEUTRIO_BAM) +
                        "--no_cmdline_in_header -o %s -L 20:10130000-10134800 " +
                        "-ERC GVCF --sample_name NA12878 -variant_index_type LINEAR " +
                        "-variant_index_parameter 128000 -A StrandAlleleCountsBySample",
                1, Arrays.asList("")
        );
        specHaplotypeCaller.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SC
        final File gVCF = executeTest("testStrandAlleleCountsBySampleHaplotypeCaller", specHaplotypeCaller).getFirst().get(0);
        List<String> gVCFList = getAttributeValues(gVCF, new String("SAC"));

        //Use gVCF from HaplotypeCaller
        final WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference),
                1,
                Arrays.asList(""));
        final File outputVCF = executeTest("testStrandAlleleCountsBySample", spec).getFirst().get(0);
        List<String> outputVCFList = getAttributeValues(outputVCF, new String("SAC"));

        // All of the SAC values in the VCF were derived from the gVCF
        Assert.assertTrue(gVCFList.containsAll(outputVCFList));
    }

    @Test
    public void testUniquifiedSamples() throws IOException {
        //two copies of 5 samples; will also test InbreedingCoeff calculation for uniquified samples
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
                        " -V:sample1B " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
                        " -V:sample2B " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
                        " -V:combined1 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                        " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                        " --uniquifySamples", b37KGReference),
                1,
                Arrays.asList("1f6321464371ecffb06108fb86ffab49"));
        executeTest("testUniquifiedSamples", spec);

    }

    /**
     * Returns a list of attribute values from a VCF file
     *
     * @param vcfFile VCF file
     * @param attributeName attribute name
     *
     * @throws IOException if the file does not exist or can not be opened
     *
     * @return list of attribute values
     */
    private List<String> getAttributeValues(final File vcfFile, final String attributeName) throws IOException {
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(vcfFile);
        final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIteratorVCF);

        List<String> attributeValues = new ArrayList<String>();
        while (lineIteratorVCF.hasNext()) {
            final String line = lineIteratorVCF.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

            for (final Genotype g : vc.getGenotypes()) {
                if (g.hasExtendedAttribute(attributeName)) {
                    attributeValues.add((String) g.getExtendedAttribute(attributeName));
                }
            }
        }

        return attributeValues;
    }

    /**
     * Section to test spanning deletions
     */
    @Test
    public void testSpanningDeletions() throws IOException {
        final String gvcf1 = privateTestDir + "spanningDel.1.g.vcf";
        final String gvcf2 = privateTestDir + "spanningDel.2.g.vcf";
        final String gvcf3 = privateTestDir + "spanningDel.3.g.vcf";

        // create the genotyped VCF to use as a basis for comparison against all of the combined versions
        // case 0: GenotypeGVCFs(1.g.vcf, 2.g.vcf, 3.g.vcf)
        final WalkerTestSpec genotypeBase = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3,
                1,
                Arrays.asList(""));
        genotypeBase.disableShadowBCF();
        final File genotypeBaseVCF = executeTest("genotypeBase", genotypeBase).getFirst().get(0);
        final List<VariantContext> BASE_VARIANT_CONTEXTS = getVariantContexts(genotypeBaseVCF);

        // case 1: GenotypeGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf), 3.g.vcf)
        final WalkerTestSpec combine12 = new WalkerTestSpec(
                "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + gvcf1 + " -V " + gvcf2,
                1,
                Arrays.asList(""));
        combine12.disableShadowBCF();
        final File combined_gVCF12 = executeTest("combine12", combine12).getFirst().get(0);
        final WalkerTestSpec genotype12_3 = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + combined_gVCF12.getAbsolutePath() + " -V " + gvcf3,
                1,
                Arrays.asList(""));
        genotype12_3.disableShadowBCF();
        final File genotype12_3VCF = executeTest("genotype12_3", genotype12_3).getFirst().get(0);
        final List<VariantContext> VARIANT_CONTEXTS_12_3 = getVariantContexts(genotype12_3VCF);
        testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_12_3);

        // case 2: GenotypeGVCFs(CombineGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf), 3.g.vcf))
        final WalkerTestSpec combine12then3 = new WalkerTestSpec(
                "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + combined_gVCF12 + " -V " + gvcf3,
                1,
                Arrays.asList(""));
        combine12then3.disableShadowBCF();
        final File combined_gVCF12then3 = executeTest("combined_gVCF12then3", combine12then3).getFirst().get(0);
        final WalkerTestSpec genotype12then3 = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + combined_gVCF12then3.getAbsolutePath(),
                1,
                Arrays.asList(""));
        genotype12then3.disableShadowBCF();
        final File genotype12then3VCF = executeTest("genotype12then3", genotype12then3).getFirst().get(0);
        final List<VariantContext> VARIANT_CONTEXTS_12then3 = getVariantContexts(genotype12then3VCF);
        testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_12then3);

        // case 3: GenotypeGVCFs(CombineGVCFs(CombineGVCFs(1.g.vcf, 3.g.vcf), 2.g.vcf))
        final WalkerTestSpec combine13 = new WalkerTestSpec(
                "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + gvcf1 + " -V " + gvcf3,
                1,
                Arrays.asList(""));
        combine13.disableShadowBCF();
        final File combined_gVCF13 = executeTest("combine13", combine13).getFirst().get(0);
        final WalkerTestSpec combine13then2 = new WalkerTestSpec(
                "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + combined_gVCF13 + " -V " + gvcf2,
                1,
                Arrays.asList(""));
        combine13then2.disableShadowBCF();
        final File combined_gVCF13then2 = executeTest("combined_gVCF13then2", combine13then2).getFirst().get(0);
        final WalkerTestSpec genotype13then2 = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + combined_gVCF13then2.getAbsolutePath(),
                1,
                Arrays.asList(""));
        genotype13then2.disableShadowBCF();
        final File genotype13then2VCF = executeTest("genotype13then2", genotype13then2).getFirst().get(0);
        final List<VariantContext> VARIANT_CONTEXTS_13then2 = getVariantContexts(genotype13then2VCF);
        testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_13then2);

        // case 4: GenotypeGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf, 3.g.vcf))
        final WalkerTestSpec combine123 = new WalkerTestSpec(
                "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3,
                1,
                Arrays.asList(""));
        combine123.disableShadowBCF();
        final File combined_gVCF123 = executeTest("combine123", combine123).getFirst().get(0);
        final WalkerTestSpec genotype123 = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + combined_gVCF123.getAbsolutePath(),
                1,
                Arrays.asList(""));
        genotype123.disableShadowBCF();
        final File genotype123VCF = executeTest("genotype123", genotype123).getFirst().get(0);
        final List<VariantContext> VARIANT_CONTEXTS_123 = getVariantContexts(genotype123VCF);
        testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_123);
    }

    /**
     * Returns a list of VariantContext records from a VCF file
     *
     * @param vcfFile VCF file
     *
     * @throws IOException if the file does not exist or can not be opened
     *
     * @return list of VariantContext records
     */
    private static List<VariantContext> getVariantContexts(final File vcfFile) throws IOException {
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(vcfFile);
        final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIteratorVCF);

        final List<VariantContext> VCs = new ArrayList<>();
        while ( lineIteratorVCF.hasNext() ) {
            final String line = lineIteratorVCF.next();
            Assert.assertFalse(line == null);
            VCs.add(codec.decode(line));
        }

        return VCs;
    }

    private static void testVCsAreEqual(final List<VariantContext> VCs1, final List<VariantContext> VCs2) {
        Assert.assertEquals(VCs1.size(), VCs2.size(), "number of Variant Contexts");
        for ( int i = 0; i < VCs1.size(); i++ ) {
            final VariantContext vc1 = VCs1.get(i);
            final VariantContext vc2 = VCs2.get(i);
            Assert.assertEquals(vc1.toStringDecodeGenotypes(), vc2.toStringDecodeGenotypes());
        }
    }


    private static final String simpleSpanningDeletionsMD5 = "9ccf64721dba002bef08046f02eb5ee9";

    @Test(enabled = true)
    public void testSpanningDeletionsMD5() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf",
                1,
                Arrays.asList(simpleSpanningDeletionsMD5));
        spec.disableShadowBCF();
        executeTest("testSpanningDeletionsMD5", spec);
    }

    @Test(enabled = true)
    public void testSpanningDeletionsFromCombinedGVCF() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "spanningDel.combined.g.vcf",
                1,
                Arrays.asList(simpleSpanningDeletionsMD5));
        spec.disableShadowBCF();
        executeTest("testSpanningDeletionsFromCombinedGVCFMD5", spec);
    }

    @Test(enabled = true)
    public void testMultipleSpanningDeletionsMD5() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf",
                1,
                Arrays.asList("80de258cf5c73e0805e15347ef82d4be"));
        spec.disableShadowBCF();
        executeTest("testMultipleSpanningDeletionsMD5", spec);
    }

    @Test(enabled = true)
    public void testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
                1,
                Arrays.asList("b16ae4b8e87bc87cd689929c28aff3de"));
        spec.disableShadowBCF();
        executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
    }

    @Test(enabled = true)
    public void testDeprecatedSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf",
                1,
                Arrays.asList("586e814c0578e245352cbb4647b5a46a"));
        spec.disableShadowBCF();
        executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
    }

    @Test(enabled = true)
    public void testGenotypingSpanningDeletionOverSpan() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                        " -V " + privateTestDir + "spanningDel.delOverSpan.1.g.vcf -V " +
                        privateTestDir + "spanningDel.delOverSpan.2.g.vcf",
                0,
                Arrays.asList(""));     // we do not care about the md5; we just want to make sure it doesn't blow up with an error
        spec.disableShadowBCF();
        executeTest("testGenotypingSpanningDeletionOverSpan", spec);
    }

    @Test(enabled = true)
    public void testBadADPropagationHaploidBugTest() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                " -V " + privateTestDir + "ad-bug-input.vcf",
                1,
                Arrays.asList("027f96584e91ca8255764fbf38293963"));
        spec.disableShadowBCF();
        executeTest("testBadADPropagationHaploidBugTest", spec);
    }
}