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

import org.broadinstitute.gatk.engine.GATKVCFUtils;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {

    final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
    final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";

    @DataProvider(name = "MyDataProviderHaploid")
    public Object[][] makeMyDataProviderHaploid() {
        List<Object[]> tests = new ArrayList<>();

        final String PCRFreeIntervals = "-L 20:10,000,000-10,010,000";
        final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;

        // this functionality can be adapted to provide input data for whatever you might want in your data
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "468b2b827297422033ccd85050ac119f"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8f31fb899458aad4d8809e98c1b19e9c"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "4f19785171b41fd01327f95af2d0385b"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "44be8f4f74a73632f2805efa6a8608e4"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "5a986c2c4f2f9b3bc1cb7bead4794d85"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "cbe35a80d1988ab9693d6d32996a34ed"});

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


    @DataProvider(name = "MyDataProvider")
    public Object[][] makeMyDataProvider() {
        List<Object[]> tests = new ArrayList<>();

        final String PCRFreeIntervals = "-L 20:10,000,000-10,010,000";
        final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;

        // this functionality can be adapted to provide input data for whatever you might want in your data
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "20f149f41438c6cc64af829cb5cd6eb6"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "381e3fed6b1826047cda2ea990b7e41f"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1d5f6804e07590850601a515c821548a"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d2b86f9be8dde27038a964cb4b87d99f"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "75d10db3eb4a65037c652830f5865dcf"});

        final String NA12878bandedResolutionMD5 = "b536f1e09d92d501fa6e891dbcafbad2";
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
        tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
                ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals + " -disableOptimizations", NA12878bandedResolutionMD5});

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

    @DataProvider(name = "MyDataProviderTetraploid")
    public Object[][] makeMyDataProviderTetraploid() {
        List<Object[]> tests = new ArrayList<>();

        final String PCRFreeIntervals = "-L 20:10,000,000-10,010,000";
        final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;

        // this functionality can be adapted to provide input data for whatever you might want in your data
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c9a85dd80f745d6433fff2c139c7158a"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "402fcd74bd6a880f7dd5b6b5acda6a33"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "ec2b1af010ba6c8e84aaa694adbee326"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1e58a154bb5f390d5a63a42955ac94da"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "b998e52a00d97ad27fb196a211205009"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "f9fdc0054819f69df30e00268d926318"});

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

    @DataProvider(name = "MyDataProviderManyploid")
    public Object[][] makeMyDataProviderManyploid() {
        List<Object[]> tests = new ArrayList<>();

        final String PCRFreeIntervals = "-L 20:10,000,000-10,010,000";
        final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;

        // this functionality can be adapted to provide input data for whatever you might want in your data
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c29c62be67c4a39a37a3bd1b4ca56c1d"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f969ca63fbb736ef0ef3a39bf9d5b48d"});
        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0272c2c5aae6aa8197711f450e604bbc"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "9ced0d30ddcabff1af2083a0fa944d9d"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "465b9ec2bfaca04adfd7abd54205a16f"});
        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "4e70638705b65c91a0a86771ec13ef74"});

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


    /**
     * Test HaplotypeCaller, using MyDataProvider
     */
    @Test(dataProvider = "MyDataProvider")
    public void testHCWithGVCF(String bam, ReferenceConfidenceMode mode, String intervals, String md5) {
        final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final String name = "testHCWithGVCF bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
        executeTest(name, spec);
    }

    /**
     * Test HaplotypeCaller with haploid samples, using MyDataProviderHaploid
     */
    @Test(dataProvider = "MyDataProviderHaploid", enabled=true)
    public void testHCWithGVCFHaploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
        final String commandLine = String.format("-T HaplotypeCaller -ploidy 1 --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final String name = "testHCWithGVCFHaploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
        executeTest(name, spec);
    }

    /**
     * Test HaplotypeCaller with tetraploid samples, using MyDataProviderTetraploid
     */
    @Test(dataProvider = "MyDataProviderTetraploid", enabled=true)
    public void testHCWithGVCFTetraploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
        final String commandLine = String.format("-T HaplotypeCaller -ploidy 4 --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final String name = "testHCWithGVCFTetraploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
        executeTest(name, spec);
    }

    /**
     * Test HaplotypeCaller with manyploid samples, using MyDataProviderManyploid
     */
    @Test(dataProvider = "MyDataProviderManyploid", enabled=true)
    public void testHCWithGVCFManyploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
        final String commandLine = String.format("-T HaplotypeCaller -ploidy 33 --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final String name = "testHCWithGVCFManyploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
        executeTest(name, spec);
    }

    @Test
    public void testERCRegionWithNoCalledHaplotypes() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
        spec.disableShadowBCF();
        executeTest("testERCRegionWithNoCalledHaplotypes", spec);
    }

    @Test()
    public void testMissingGVCFIndexException() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
        spec.disableShadowBCF();
        executeTest("testMissingGVCFIndexingStrategyException", spec);
    }

    /**
     * Test HaplotypeCaller to ensure it does not throw an exception when a .g.vcf output file is specified and the indexing arguments are omitted
     */
    @Test()
    public void testGVCFIndexNoThrow() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000000-17000100");
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine  + " -o %s", Arrays.asList(GATKVCFUtils.GVCF_EXT), Arrays.asList(""));
        spec.disableShadowBCF();
        executeTest("testGVCFIndexNoThrow", spec);
    }

    /**
     * Test HaplotypeCaller to ensure it does not throw an exception when a .g.vcf.gz output file is specified and the indexing arguments are omitted
     */
    @Test()
    public void testGVCFGzIndexNoThrow() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000000-17000100");
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine  + " -o %s", Arrays.asList(GATKVCFUtils.GVCF_GZ_EXT), Arrays.asList(""));
        spec.disableShadowBCF();
        executeTest("testGVCFIndexNoThrow", spec);
    }

    @Test()
    public void testWrongParameterGVCFIndexException() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER + 1);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
        spec.disableShadowBCF();
        executeTest("testMissingGVCFIndexingStrategyException", spec);
    }

    @Test()
    public void testWrongTypeGVCFIndexException() {
        // ensure non-optimal, if optimal changes
        GATKVCFIndexType type = GATKVCFIndexType.DYNAMIC_SEEK;
        if (GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE == GATKVCFIndexType.DYNAMIC_SEEK)
            type = GATKVCFIndexType.DYNAMIC_SIZE;

        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
        spec.disableShadowBCF();
        executeTest("testMissingGVCFIndexingStrategyException", spec);
    }

    private final static String WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS = privateTestDir + "gvcf_unsorted_records_bug.interval_list";
    private final static String WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM = privateTestDir + "gvcf_unsorted_records_bug.bam";

    @Test()
    public void testWrongGVCFNonVariantRecordOrderBugFix() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e2de7ac5456a14122eaa910e6b3c4cc9"));
        spec.disableShadowBCF();
        executeTest("testMissingGVCFIndexingStrategyException", spec);
    }

    private static final String NOCALL_GVCF_BUGFIX_INTERVALS = privateTestDir + "gvcf_nocall_bug.interval_list";
    private static final String NOCALL_GVCF_BUGFIX_BAM = privateTestDir + "gvcf_nocall_bug.bam";
    private static final String GENERAL_PLOIDY_BUGFIX1_BAM = privateTestDir + "general-ploidy-arrayindex-bug-1.bam";
    private static final String GENERAL_PLOIDY_BUGFIX1_INTERVALS = privateTestDir + "general-ploidy-arrayindex-bug-1.intervals";
    private static final String GENERAL_PLOIDY_BUGFIX2_BAM = privateTestDir + "general-ploidy-arrayindex-bug-2.bam";
    private static final String GENERAL_PLOIDY_BUGFIX2_INTERVALS = privateTestDir + "general-ploidy-arrayindex-bug-2.intervals";


    @Test
    public void testNoCallGVCFMissingPLsBugFix() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c8d5b833fa79da1270b7fe64ebea0763"));
        spec.disableShadowBCF();
        executeTest("testNoCallGVCFMissingPLsBugFix", spec);
    }

    /**
     * Checking that the bug's Exception is no longer been thrown (thus no md5).
     */
    @Test(enabled=true)
    public void testGeneralPloidyArrayIndexBug1Fix() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 1 -maxAltAlleles 2 -isr INTERSECTION -L 1:23696115-23696189",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, GENERAL_PLOIDY_BUGFIX1_BAM, GENERAL_PLOIDY_BUGFIX1_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
        spec.disableShadowBCF();
        executeTest(" testGeneralPloidyArrayIndexBug1Fix", spec);
    }

    /**
     * Checking that the bug's Exception is no longer been thrown (thus no md5).
     */
    @Test(enabled=true)
    public void testGeneralPloidyArrayIndexBug2Fix() {
        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 2 -maxAltAlleles 2 -A DepthPerSampleHC -A StrandBiasBySample -L 1:38052860-38052937",
                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, GENERAL_PLOIDY_BUGFIX2_BAM, GENERAL_PLOIDY_BUGFIX2_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
        spec.disableShadowBCF();
        executeTest(" testGeneralPloidyArrayIndexBug2Fix", spec);
    }

}
