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

import htsjdk.samtools.util.BlockCompressedInputStream;
import htsjdk.tribble.readers.AsciiLineReader;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.engine.GATKVCFUtils;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.Test;

import java.io.File;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;

// ********************************************************************************** //
// Note that this class also serves as an integration test for the VariantAnnotator!  //
// ********************************************************************************** //

public class UnifiedGenotyperIntegrationTest extends WalkerTest {

    private final static String baseCommand = "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
    private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing parameters
    //
    // --------------------------------------------------------------------------------------------------------------

    @Test
    public void testMinBaseQualityScore() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
                Arrays.asList("24e3de56a64cf50e1ce159c640d2a914"));
        executeTest("test min_base_quality_score 26", spec);
    }

    @Test
    public void testSLOD() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
                Arrays.asList("500036226dd2dfb3593b8c203d818e28"));
        executeTest("test SLOD", spec);
    }

    @Test
    public void testNDA() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
                Arrays.asList("f04503b889f4510023f00082afe65079"));
        executeTest("test NDA", spec);
    }

    @Test
    public void testCompTrack() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
                Arrays.asList("7c9a4c9283185d6d0e5263040cd04527"));
        executeTest("test using comp track", spec);
    }

    @Test(enabled = false) // EB: for some reason this test crashes whenever I run it on my local machine
    public void testNoCmdLineHeaderStdout() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommandNoCmdLineHeaderStdout + " -glm INDEL -L 1:67,225,396-67,288,518", 0,
                Collections.<String>emptyList());
        executeTest("testNoCmdLineHeaderStdout", spec);
    }

    @Test
    public void testOutputParameterSitesOnly() {
        testOutputParameters("-sites_only", "433df49e8ba3bfa3b32ff165b717ab51");
    }

    @Test
    public void testOutputParameterAllConfident() {
        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "5628f9829474896fcc3a743d92f8300f");
    }

    @Test
    public void testOutputParameterAllSites() {
        testOutputParameters("--output_mode EMIT_ALL_SITES", "4371fd83cc4904d60b943a7777e8e292");
    }

    private void testOutputParameters(final String args, final String md5) {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 " + args, 1,
                Arrays.asList(md5));
        executeTest(String.format("testParameter[%s]", args), spec);
    }

    @Test
    public void testConfidence() {
        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
                Arrays.asList("a1d212a5d23400f29517a4f25bff2fe2"));
        executeTest("test confidence 1", spec1);
    }

    @Test
    public void testNoPrior() {
        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.33333 -inputPrior 0.33333", 1,
                Arrays.asList("32b02c0315248dd69f19000f0a9687bb"));
        executeTest("test no prior 1", spec1);

    }

    @Test
    public void testUserPrior() {
        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.001 -inputPrior 0.495", 1,
                Arrays.asList("5b6576518c62fab480252311dae8e716"));
        executeTest("test user prior 1", spec1);

    }

    @Test
    public void emitPLsAtAllSites() {
        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
                Arrays.asList("c9074a9ea9aa1ec42fc71cc1bc6b589f"));
        // GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
        spec1.disableShadowBCF();

        executeTest("test all site PLs 1", spec1);

    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing heterozygosity
    //
    // --------------------------------------------------------------------------------------------------------------

    @Test
    public void testHeterozyosity1() {
        testHeterozosity( 0.01, "c7f8684e4cb3175f274f91f80573d910" );
    }

    @Test
    public void testHeterozyosity2() {
        testHeterozosity( 1.0 / 1850, "1f067c6442dbccf5c341ea1a41e9d28b" );
    }

    private void testHeterozosity(final double arg, final String md5) {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000 --heterozygosity " + arg, 1,
                Arrays.asList(md5));
        executeTest(String.format("test heterozyosity[%s]", arg), spec);
    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing compressed output
    //
    // --------------------------------------------------------------------------------------------------------------

    /*
    TODO:   This test needs to be rewritten. Currently when the md5 changes the test errors out with
                htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header:
            when it tries to read in the nonexistent output file instead of just giving the new md5 like all the other tests.

    private final static String COMPRESSED_OUTPUT_MD5 = "c5c6af421cffa12fe6bdaced6cd41dd2";

    @Test
    public void testCompressedOutput() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
                Arrays.asList("gz"), Arrays.asList(COMPRESSED_OUTPUT_MD5));
        executeTest("test compressed output", spec);
    }
    */

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing parallelization
    //
    // --------------------------------------------------------------------------------------------------------------

    @Test
    public void testParallelization() {

        // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations

        String md5 = "398d3ad38834fea8961ab6f46a21dc4b";
        final String myCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;

        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                myCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
                Arrays.asList(md5));
        executeTest("test parallelization (single thread)", spec1);

        Utils.resetRandomGenerator();

        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                myCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
                Arrays.asList(md5));
        executeTest("test parallelization (2 threads)", spec2);

        Utils.resetRandomGenerator();

        WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
                myCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
                Arrays.asList(md5));
        executeTest("test parallelization (4 threads)", spec3);
    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing calls with SLX, 454, and SOLID data
    //
    // --------------------------------------------------------------------------------------------------------------
    @Test
    public void testMultiTechnologies() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand +
                        " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
                        " -o %s" +
                        " -L 1:10,000,000-10,100,000",
                1,
                Arrays.asList("ac54cc421a4c8a441179cd85653715a7"));

        executeTest(String.format("test multiple technologies"), spec);
    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing calls with BAQ
    //
    // --------------------------------------------------------------------------------------------------------------
    @Test
    public void testCallingWithBAQ() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand +
                        " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
                        " -o %s" +
                        " -L 1:10,000,000-10,100,000" +
                        " -baq CALCULATE_AS_NECESSARY",
                1,
                Arrays.asList("f561ce9ab992c99caea934fa7d649ee6"));

        executeTest(String.format("test calling with BAQ"), spec);
    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing SnpEff
    //
    // --------------------------------------------------------------------------------------------------------------

    @Test
    public void testSnpEffAnnotationRequestedWithoutRodBinding() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
                "-A SnpEff",
                1,
                Arrays.asList("42c2d98ed221b30b6a8986ce65b13066"));
        executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing Ns in CIGAR
    //
    // --------------------------------------------------------------------------------------------------------------

    @Test
    public void testNsInCigar() {
        final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "testWithNs.bam -o %s -L 8:141813600-141813700 -out_mode EMIT_ALL_SITES", 1,
                UserException.UnsupportedCigarOperatorException.class);

        executeTest("test calling on reads with Ns in CIGAR", spec);
    }

    @Test(enabled = true)
    public void testCompressedVCFOutputWithNT() throws Exception {
        WalkerTestSpec spec = new WalkerTestSpec("-T UnifiedGenotyper -R " + b37KGReference + " -I "
                + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam"
                + " -o %s -L 20:10,000,000-10,100,000 -nt 4",
                1, Arrays.asList("vcf.gz"), Arrays.asList(""));
        final File vcf = executeTest("testCompressedVCFOutputWithNT", spec).first.get(0);
        final AsciiLineReader reader = new AsciiLineReader(new BlockCompressedInputStream(vcf));
        int nLines = 0;
        while ( reader.readLine() != null )
            nLines++;
        Assert.assertTrue(nLines > 0);
    }

    // --------------------------------------------------------------------------------------------------------------
    //
    // testing only emit samples
    //
    // --------------------------------------------------------------------------------------------------------------

    @Test(enabled = true)
    public void testOnlyEmitSample() throws Exception {
        final String base = "-T UnifiedGenotyper -R " + b37KGReference + " -I "
                + privateTestDir + "AFR.complex.variants.bam --disableDithering"
                + " -o %s -L 20:10,000,000-10,100,000";
        final WalkerTestSpec specAllSamples = new WalkerTestSpec(base, 1, Arrays.asList(""));
        specAllSamples.disableShadowBCF();
        final File allSamplesVCF = executeTest("testOnlyEmitSampleAllSamples", specAllSamples).first.get(0);
        final List<VariantContext> allSampleVCs = GATKVCFUtils.readVCF(allSamplesVCF).getSecond();

        final WalkerTestSpec onlyHG01879 = new WalkerTestSpec(base + " -onlyEmitSamples HG01879", 1, Arrays.asList(""));
        onlyHG01879.disableShadowBCF();
        final File onlyHG01879VCF = executeTest("testOnlyEmitSample", onlyHG01879).first.get(0);
        final List<VariantContext> onlyHG01879VCs = GATKVCFUtils.readVCF(onlyHG01879VCF).getSecond();

        Assert.assertEquals(allSampleVCs.size(), onlyHG01879VCs.size());
        for ( int i = 0; i < allSampleVCs.size(); i++ ) {
            final VariantContext allSampleVC = allSampleVCs.get(i);
            final VariantContext onlyHG01879VC = onlyHG01879VCs.get(i);

            if ( allSampleVC == null ) {
                Assert.assertNull(onlyHG01879VC);
            } else {
                Assert.assertNotNull(onlyHG01879VC);

                Assert.assertTrue(allSampleVC.getGenotypes().size() > 1, "All samples should have had more than 1 genotype, but didn't");
                Assert.assertEquals(onlyHG01879VC.getGenotypes().size(), 1, "Should have found a single sample genotype, but didn't");
                Assert.assertEquals(onlyHG01879VC.hasGenotype("HG01879"), true);

                Assert.assertEquals(allSampleVC.getStart(), onlyHG01879VC.getStart());
                Assert.assertEquals(allSampleVC.getChr(), onlyHG01879VC.getChr());
                Assert.assertEquals(allSampleVC.getEnd(), onlyHG01879VC.getEnd());
                Assert.assertEquals(allSampleVC.getFilters(), onlyHG01879VC.getFilters());
                Assert.assertEquals(allSampleVC.getAlleles(), onlyHG01879VC.getAlleles());
                Assert.assertEquals(allSampleVC.getAttributes(), onlyHG01879VC.getAttributes());
                Assert.assertEquals(allSampleVC.getPhredScaledQual(), onlyHG01879VC.getPhredScaledQual());

                final Genotype allG = allSampleVC.getGenotype("HG01879");
                final Genotype onlyG = onlyHG01879VC.getGenotype("HG01879");
                Assert.assertEquals(allG.getAD(), onlyG.getAD());
                Assert.assertEquals(allG.getDP(), onlyG.getDP());
                Assert.assertEquals(allG.getAlleles(), onlyG.getAlleles());
                Assert.assertEquals(allG.getPL(), onlyG.getPL());
                Assert.assertEquals(allG.toString(), onlyG.toString());
            }
        }
    }
}
