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

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

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

/**
 * @author ebanks
 * @since 7/16/12
 */
public class BQSRIntegrationTest extends WalkerTest {

    private static class BQSRTest {
        final String reference;
        final String interval;
        final String bam;
        final String args;
        final String md5;

        private BQSRTest(String reference, String bam, String interval, String args, String md5) {
            this.reference = reference;
            this.bam = bam;
            this.interval = interval;
            this.args = args;
            this.md5 = md5;
        }

        public String getCommandLine() {
            return " -T BaseRecalibrator" +
                    " -R " + reference +
                    " -I " + bam +
                    " -L " + interval +
                    args +
                    " -knownSites " + (reference.equals(b36KGReference) ? b36dbSNP129 : (reference.equals(b37KGReference) ? b37dbSNP129 : hg18dbSNP132)) +
                    " --allow_potentially_misencoded_quality_scores" +  // TODO -- remove me when we get new SOLiD bams
                    " -o %s" +
                    " -sortAllCols";
        }

        @Override
        public String toString() {
            return String.format("BQSR(bam='%s', args='%s')", bam, args);
        }
    }

    private static final String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
    private static final String HiSeqInterval = "chr1:10,000,000-10,100,000";
    private static final String SimpleCigarMatchMismatchBam = privateTestDir + "simpleCigarMatchMismatch.bam";
    private static final String SimpleCigarMatchMismatchInterval = "1:1-60";

    @DataProvider(name = "BQSRTest")
    public Object[][] createBQSRTestData() {
        return new Object[][]{
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "fc9df1faf67bab70d32f89bcf4fa39db")},
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "73ec38eb23b1739ecef8194cbb1132a3")},
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "2d5721193ed4410d1a7d8db467a1fa05")},
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "16df7f1745f17f190c9fc33c475b91d8")},
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "01811003ae811ee74c4b8d3eb5e992fe")},
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "5e0eea6b0b300fbd2edabc3506ad3a60")},
                {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "8500b9747c16cb8eb17082163bdb8069")},
                {new BQSRTest(b36KGReference, SimpleCigarMatchMismatchBam, SimpleCigarMatchMismatchInterval, "", "56dfb2918a4cdae3ef9d705a43e85194")},
                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "0b5a8e259e997e4c7b5836d4c28e6f4d")},
                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "281682124584ab384f23359934df0c3b")},
                {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "0a92fdff5fd26227c29d34eda5a32f49")},
                {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "90d8c24077e8ae9a0037a9aad5f09e31")},
                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "c41ef02c640ef1fed4bfc03b9b33b616")},
                {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "b577cd1d529425f66db49620db09fdca")},
                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "0b5a8e259e997e4c7b5836d4c28e6f4d")},
                {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "9ad49269c0156f8ab1173261bf23e600")},
                // make sure we work with ION torrent bam
                {new BQSRTest(b37KGReference, privateTestDir + "iontorrent.bam", "20:10,000,000-10,200,000", "", "04bfa4760767022e7f5252e6e4432cc1")},
        };
    }

    @Test(dataProvider = "BQSRTest")
    public void testBQSR(BQSRTest params) {
        WalkerTestSpec spec = new WalkerTestSpec(
                params.getCommandLine(),
                Arrays.asList(params.md5));
        executeTest("testBQSR-"+params.args, spec).getFirst();
    }

    @Test
    public void testBQSRFailWithoutDBSNP() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                " -T BaseRecalibrator" +
                        " -R " + b36KGReference +
                        " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
                        " -L 1:10,000,000-10,200,000" +
                        " -o %s",
                1, // just one output file
                UserException.CommandLineException.class);
        executeTest("testBQSRFailWithoutDBSNP", spec);
    }

    @Test
    public void testBQSRFailWithSolidNoCall() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                " -T BaseRecalibrator" +
                        " -R " + b36KGReference +
                        " -I " + privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam" +
                        " -L 1:50,000-80,000" +
                        " --allow_potentially_misencoded_quality_scores" +  // TODO -- remove me when we get new SOLiD bams
                        " -o %s" +
                        " -sortAllCols",
                1, // just one output file
                UserException.class);
        executeTest("testBQSRFailWithSolidNoCall", spec);
    }

    @Test
    public void testBQSRFailWithReducedBam() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                " -T BaseRecalibrator" +
                        " -R " + b37KGReference +
                        " -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam" +
                        " -L 1:67,225,396-67,288,518" +
                        " -o /dev/null",
                0,
                UserException.class);
        executeTest("testBQSRFailWithReducedBam", spec);
    }

    private static class PRTest {
        final String args;
        final String md5;

        private PRTest(String args, String md5) {
            this.args = args;
            this.md5 = md5;
        }

        @Override
        public String toString() {
            return String.format("PrintReads(args='%s')", args);
        }
    }

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

        tests.add(new Object[]{1, new PRTest(" -qq -1", "8a38828e3b14ce067614d4248e3ea95a")});
        tests.add(new Object[]{1, new PRTest(" -qq 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")});
        tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")});

        for ( final int nct : Arrays.asList(1, 2, 4) ) {
            tests.add(new Object[]{nct, new PRTest("", "6451093cadfc14d7359617b2a7ea6db8")});
        }

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

    @Test(dataProvider = "PRTest")
    public void testPR(final int nct, PRTest params) {
        WalkerTestSpec spec = new WalkerTestSpec(
                "-T PrintReads" +
                        " -R " + hg18Reference +
                        " -I " + privateTestDir + "HiSeq.1mb.1RG.bam" +
                        " -nct " + nct +
                        " --no_pg_tag" +
                        " -BQSR " + privateTestDir + "HiSeq.20mb.1RG.table" +
                        params.args +
                        " -o %s",
                Arrays.asList(params.md5));
        executeTest("testPrintReads-"+params.args, spec).getFirst();
    }

    @Test
    public void testPRNoFailWithHighMaxCycle() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                " -T PrintReads" +
                        " -R " + hg18Reference +
                        " -I " + HiSeqBam +
                        " -L " + HiSeqInterval +
                        " --no_pg_tag" +
                        " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.highMaxCycle.table" +
                        " -o /dev/null",
                0,
                Arrays.<String>asList());
        executeTest("testPRNoFailWithHighMaxCycle", spec);
    }

    @Test
    public void testPRFailWithLowMaxCycle() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                " -T PrintReads" +
                        " -R " + hg18Reference +
                        " -I " + HiSeqBam +
                        " -L " + HiSeqInterval +
                        " --no_pg_tag" +
                        " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
                        " -o /dev/null",
                0,
                UserException.class);
        executeTest("testPRFailWithLowMaxCycle", spec);
    }

    @Test
    public void testPRFailWithBadPL() {
        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                " -T BaseRecalibrator" +
                        " -R " + b37KGReference +
                        " -I " + privateTestDir + "badPLForBQSR.bam" +
                        " -L 1:10,000,000-10,200,000" +
                        " -o %s",
                1,
                UserException.class);
        executeTest("testPRFailWithBadPL", spec);
    }
}
