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

import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.testng.annotations.Test;

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

/**
 * Tests CombineVariants
 */
public class CombineVariantsIntegrationTest extends WalkerTest {
    //
    // TODO TODO TODO TODO TODO TODO TODO TODO
    // TODO TODO TODO TODO TODO TODO TODO TODO
    //
    // TODO WHEN THE HC EMITS VALID VCF HEADERS ENABLE BCF AND REMOVE lenientVCFProcessing ARGUMENTS
    //
    // TODO TODO TODO TODO TODO TODO TODO TODO
    // TODO TODO TODO TODO TODO TODO TODO TODO
    // TODO TODO TODO TODO TODO TODO TODO TODO
    //
    private static String baseTestString(String args) {
        return baseTestString(args, b36KGReference);
    }

    private static String baseTestString(String args, String ref) {
        return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + ref + args;
        //return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -U LENIENT_VCF_PROCESSING -R " + b36KGReference + args;
    }

    private void cvExecuteTest(final String name, final WalkerTestSpec spec, final boolean parallel) {
        spec.disableShadowBCF();
        if ( parallel )
            executeTestParallel(name, spec);
        else
            executeTest(name, spec);
    }

    public void test1InOut(String file, String md5) {
        test1InOut(file, md5, "");
    }

    public void test1InOut(String file, String md5, String args) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -priority v1 -V:v1 " + validationDataLocation + file + args),
                 1,
                 Arrays.asList(md5));
         cvExecuteTest("testInOut1--" + file, spec, true);
    }

    public void combine2(String file1, String file2, String args, String md5) {
        combine2(file1, file2, args, md5, true);
    }

    public void combine2(String file1, String file2, String args, String md5, final boolean parallel) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 "+ validationDataLocation + file2 + args),
                 1,
                 Arrays.asList(md5));
         cvExecuteTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, parallel);
    }

    public void combineSites(String args, String md5) {
        String file1 = "1000G_omni2.5.b37.sites.vcf";
        String file2 = "hapmap_3.3.b37.sites.vcf";
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T CombineVariants --no_cmdline_in_header -o %s -R " + b37KGReference
                        + " -L 1:1-10,000,000 -V:omni " + validationDataLocation + file1
                        + " -V:hm3 " + validationDataLocation + file2 + args,
                1,
                Arrays.asList(md5));
        cvExecuteTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true);
    }

    public void combinePLs(String file1, String file2, String md5) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T CombineVariants --no_cmdline_in_header -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + privateTestDir + file1 + " -V:v2 " + privateTestDir + file2,
                 1,
                 Arrays.asList(md5));
         cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, true);
    }

    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e3dbdfa14aefb2f6bd1213287d34a2e5", " -U LENIENT_VCF_PROCESSING"); }
    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "d727fab83b4265859c4a902f6e66ac3d", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "42fc3d2c68415a61ff15e594a63d9349", " -setKey null -U LENIENT_VCF_PROCESSING"); }
    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "a3994d6145bb3813950939238db4c592"); } // official project VCF files in tabix format

    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "e7fd959312e2aff0b4231963ee690aec"); }
    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "23439a1f0108b57a14e18efe9482cc88"); }

    @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "27aa46cdb022be3959e7240a0d7ac794"); }

    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9bdda937754e1407183406808f560723"); } // official project VCF files in tabix format
    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "6344953a82a422115bd647ec1d696b94"); } // official project VCF files in tabix format
    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c4b995405872b22ded76c0a9e183c52d"); }

    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f9d1d7e6246f0ce9e493357d5b320323"); }

    @Test public void uniqueSNPs() {
        // parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s
        //both of these files have the YRI trio and merging of duplicate samples without priority must be specified with UNSORTED merge type
        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "5aece78046bfb7d6ee8dc4d551542e3a", true);
    }

    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "0897efcc0046bd94760315838d4d0fa5"); }
    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "8b12b09a6ec4e3fde2352bbf82637f1e"); }

    @Test public void threeWayWithRefs() {
        WalkerTestSpec spec = new WalkerTestSpec(
                baseTestString(" -V:NA19240_BGI "+validationDataLocation+"NA19240.BGI.RG.vcf" +
                        " -V:NA19240_ILLUMINA "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
                        " -V:NA19240_WUGSC "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
                        " -V:denovoInfo "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
                        " -setKey centerSet" +
                        " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
                        " -U LENIENT_VCF_PROCESSING" +
                        " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                        " -genotypeMergeOptions UNIQUIFY -L 1"),
                1,
                Arrays.asList("8f8ba6d671f67386883c11873df3cf95"));
        cvExecuteTest("threeWayWithRefs", spec, true);
    }

    // complex examples with filtering, indels, and multiple alleles
    public void combineComplexSites(String args, String md5) {
        String file1 = "combine.1.vcf";
        String file2 = "combine.2.vcf";
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T CombineVariants --no_cmdline_in_header -o %s -R " + b37KGReference
                        + " -V:one " + privateTestDir + file1
                        + " -V:two " + privateTestDir + file2 + args,
                1,
                Arrays.asList(md5));
        cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true);
    }

    @Test public void complexTestFull() { combineComplexSites("", "3a702773e31674b14a1073d455f6f1ce"); }
    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "cabad0e328f1c967d44aaf2085da5dcf"); }
    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "31f6f62664cc5891e9a8e228dbb6278d"); }
    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "31f6f62664cc5891e9a8e228dbb6278d"); }

    @Test
    public void combineDBSNPDuplicateSites() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
                 1,
                 Arrays.asList("b0d4b86702b44fc4faa527c34adf6239"));
         cvExecuteTest("combineDBSNPDuplicateSites:", spec, true);
    }

    @Test
    public void combineLeavesUnfilteredRecordsUnfiltered() {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T CombineVariants --no_cmdline_in_header -o %s "
                        + " -R " + b37KGReference
                        + " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf",
                1,
                Arrays.asList("11aab642395645589e48edee1fb179e2"));
        cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
    }

    @Test
    public void combiningGVCFsFails() {
        try {
            WalkerTestSpec spec = new WalkerTestSpec(
                    "-T CombineVariants --no_cmdline_in_header -o %s "
                            + " -R " + b37KGReference
                            + " -V " + privateTestDir + "gvcfExample1.vcf",
                    1,
                    Arrays.asList("FAILFAILFAILFAILFAILFAILFAILFAIL"));
            executeTest("combiningGVCFsFails", spec);
        } catch (Exception e) { } // do nothing
    }

    @Test
    public void combineSymbolicVariants() {
        // Just checking that this does not fail, hence no output files and MD5
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T CombineVariants --no_cmdline_in_header -o %s "
                        + " -R " + hg19RefereneWithChrPrefixInChromosomeNames
                        + " -V " + privateTestDir + "WES-chr1.DEL.vcf"
                        + " -V " + privateTestDir + "WGS-chr1.DEL.vcf"
                        + " -genotypeMergeOptions UNIQUIFY",
                0,
                Arrays.asList(""));
        executeTest("combineSymbolicVariants: ", spec);
    }
}