/*
 * The MIT License
 *
 * Copyright (c) 2015 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package picard.analysis;

import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.filter.DuplicateReadFilter;
import htsjdk.samtools.filter.InsertSizeFilter;
import htsjdk.samtools.filter.NotPrimaryAlignmentFilter;
import htsjdk.samtools.filter.SamRecordFilter;
import htsjdk.samtools.metrics.MetricBase;
import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.reference.ReferenceSequenceFileWalker;
import htsjdk.samtools.util.*;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
import picard.util.DbSnpBitSetUtil;
import picard.util.help.HelpConstants;
import picard.util.SequenceDictionaryUtils;

import java.io.File;
import java.util.*;
import java.lang.Math;


/**
 * Class for trying to quantify the CpCG->CpCA error rate.
 */
@CommandLineProgramProperties(
        summary = CollectOxoGMetrics.USAGE_SUMMARY + CollectOxoGMetrics.USAGE_DETAILS,
        oneLineSummary = CollectOxoGMetrics.USAGE_SUMMARY,
        programGroup = DiagnosticsAndQCProgramGroup.class
)
@DocumentedFeature
public class CollectOxoGMetrics extends CommandLineProgram {
    static final String USAGE_SUMMARY = "Collect metrics to assess oxidative artifacts.";
    static final String USAGE_DETAILS = "This tool collects metrics quantifying the error rate resulting from oxidative artifacts. " +
            "For a brief primer on oxidative artifacts, see " +
            "<a href='http://gatkforums.broadinstitute.org/discussion/6328/oxog-oxidative-artifacts'>" +
            "the GATK Dictionary</a>." +
            "<br /><br />" +
            "This tool calculates the Phred-scaled probability that an alternate base call results from an oxidation artifact. This " +
            "probability score is based on base context, sequencing read orientation, and the characteristic low allelic frequency.  " +
            "Please see the following reference for an in-depth " +
            "<a href='http://nar.oxfordjournals.org/content/early/2013/01/08/nar.gks1443'>discussion</a>" +
            " of the OxoG error rate.  " +
            "<p>Lower probability values implicate artifacts resulting from 8-oxoguanine, while higher " +
            "probability values suggest that an alternate base call is due to either some other type of artifact or is a " +
            "real variant.</p>" +
            "<h4>Usage example:</h4>" +
            "<pre>" +
            "java -jar picard.jar CollectOxoGMetrics \\<br />" +
            "      I=input.bam \\<br />" +
            "      O=oxoG_metrics.txt \\<br />" +
            "      R=reference_sequence.fasta" +
            "</pre>" +
            "" +
            "<hr />";
    @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME,
            doc = "Input SAM/BAM/CRAM file for analysis.")
    public File INPUT;

    @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,
            doc = "Location of output metrics file to write.")
    public File OUTPUT;

    @Argument(doc = "An optional list of intervals to restrict analysis to.",
            optional = true)
    public File INTERVALS;

    @Argument(doc = "VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.",
            optional = true)
    public File DB_SNP;

    @Argument(shortName = "Q",
            doc = "The minimum base quality score for a base to be included in analysis.")
    public int MINIMUM_QUALITY_SCORE = 20;

    @Argument(shortName = StandardOptionDefinitions.MINIMUM_MAPPING_QUALITY_SHORT_NAME,
            doc = "The minimum mapping quality score for a base to be included in analysis.")
    public int MINIMUM_MAPPING_QUALITY = 30;

    @Argument(shortName = "MIN_INS",
            doc = "The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
    public int MINIMUM_INSERT_SIZE = 60;

    @Argument(shortName = "MAX_INS",
            doc = "The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
    public int MAXIMUM_INSERT_SIZE = 600;

    @Argument(shortName = "NON_PF", doc = "Whether or not to include non-PF reads.")
    public boolean INCLUDE_NON_PF_READS = true;

    @Argument(doc = "When available, use original quality scores for filtering.")
    public boolean USE_OQ = true;

    @Argument(doc = "The number of context bases to include on each side of the assayed G/C base.")
    public int CONTEXT_SIZE = 1;

    @Argument(doc = "The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.", optional = true)
    public Set<String> CONTEXTS = new HashSet<>();

    @Argument(doc = "For debugging purposes: stop after visiting this many sites with at least 1X coverage.")
    public int STOP_AFTER = Integer.MAX_VALUE;

    private final Log log = Log.getInstance(CollectOxoGMetrics.class);
    private static final String UNKNOWN_LIBRARY = "UnknownLibrary";
    private static final String UNKNOWN_SAMPLE = "UnknownSample";

    /** Metrics class for outputs. */
    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
    public static final class CpcgMetrics extends MetricBase {
        /** The name of the sample being assayed. */
        public String SAMPLE_ALIAS;
        /** The name of the library being assayed. */
        public String LIBRARY;
        /** The sequence context being reported on. */
        public String CONTEXT;
        /** The total number of sites that had at least one base covering them. */
        public int TOTAL_SITES;
        /** The total number of basecalls observed at all sites. */
        public long TOTAL_BASES;
        /** The number of reference alleles observed as C in read 1 and G in read 2. */
        public long REF_NONOXO_BASES;
        /** The number of reference alleles observed as G in read 1 and C in read 2. */
        public long REF_OXO_BASES;
        /** The total number of reference alleles observed */
        public long REF_TOTAL_BASES;
        /**
         * The count of observed A basecalls at C reference positions and T basecalls
         * at G reference bases that are correlated to instrument read number in a way
         * that rules out oxidation as the cause
         */
        public long ALT_NONOXO_BASES;
        /**
         * The count of observed A basecalls at C reference positions and T basecalls
         * at G reference bases that are correlated to instrument read number in a way
         * that is consistent with oxidative damage.
         */
        public long ALT_OXO_BASES;
        /** The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES */
        public double OXIDATION_ERROR_RATE;
        /** -10 * log10(OXIDATION_ERROR_RATE) */
        public double OXIDATION_Q;

        // Fields below this point are metrics that are calculated to see if there is oxidative damage that is
        // biased toward the reference base - i.e. occurs more where the reference base is a C vs. a G or vice
        // versa.

        /** The number of ref basecalls observed at sites where the genome reference == C. */
        public long C_REF_REF_BASES;
        /** The number of ref basecalls observed at sites where the genome reference == G. */
        public long G_REF_REF_BASES;
        /** The number of alt (A/T) basecalls observed at sites where the genome reference == C. */
        public long C_REF_ALT_BASES;
        /** The number of alt (A/T) basecalls observed at sites where the genome reference == G. */
        public long G_REF_ALT_BASES;

        /**
         * The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there
         * were no bias between sites with a C reference base vs. a G reference base.
         */
        public double C_REF_OXO_ERROR_RATE;
        /** C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. */
        public double C_REF_OXO_Q;
        /**
         * The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there
         * were no bias between sites with a C reference base vs. a G reference base.
         */
        public double G_REF_OXO_ERROR_RATE;
        /** G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. */
        public double G_REF_OXO_Q;
    }

    @Override
    protected boolean requiresReference() {
        return true;
    }

    @Override
    protected String[] customCommandLineValidation() {
        final int size = 1 + 2 * CONTEXT_SIZE;
        final List<String> messages = new ArrayList<>();

        for (final String ctx : CONTEXTS) {
            if (ctx.length() != size) {
                messages.add("Context " + ctx + " is not " + size + " long as implied by CONTEXT_SIZE=" + CONTEXT_SIZE);
            } else if (ctx.charAt(ctx.length() / 2) != 'C') {
                messages.add("Middle base of context sequence " + ctx + " must be C");
            }
        }

        if (MINIMUM_INSERT_SIZE < 0) messages.add("MINIMUM_INSERT_SIZE cannot be negative");
        if (MAXIMUM_INSERT_SIZE < 0) messages.add("MAXIMUM_INSERT_SIZE cannot be negative");
        if (MAXIMUM_INSERT_SIZE < MINIMUM_INSERT_SIZE) {
            messages.add("MAXIMUM_INSERT_SIZE cannot be less than MINIMUM_INSERT_SIZE");
        }

        return messages.isEmpty() ? null : messages.toArray(new String[messages.size()]);
    }

    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);
        if (INTERVALS != null) IOUtil.assertFileIsReadable(INTERVALS);
        IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);

        final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);

        if (!in.getFileHeader().getSequenceDictionary().isEmpty()) {
            SequenceDictionaryUtils.assertSequenceDictionariesEqual(
                    in.getFileHeader().getSequenceDictionary(),
                    INPUT.getAbsolutePath(),
                    refWalker.getSequenceDictionary(),
                    REFERENCE_SEQUENCE.getAbsolutePath());
        }

        final Set<String> samples = new HashSet<>();
        final Set<String> libraries = new HashSet<>();
        
        if (in.getFileHeader().getReadGroups().isEmpty()) {
            throw new PicardException("This analysis requires a read group entry in the alignment file header");
        }
        
        for (final SAMReadGroupRecord rec : in.getFileHeader().getReadGroups()) {
            samples.add(Optional.ofNullable(rec.getSample()).orElse(UNKNOWN_SAMPLE));
            libraries.add(Optional.ofNullable(rec.getLibrary()).orElse(UNKNOWN_LIBRARY));
        }

        // Setup the calculators
        final Set<String> contexts = CONTEXTS.isEmpty() ? makeContextStrings(CONTEXT_SIZE) : CONTEXTS;
        final ListMap<String, Calculator> calculators = new ListMap<>();
        for (final String context : contexts) {
            for (final String library : libraries) {
                calculators.add(context, new Calculator(library, context));
            }
        }

        // Load up dbSNP if available
        log.info("Loading dbSNP File: " + DB_SNP);
        final DbSnpBitSetUtil dbSnp;
        if (DB_SNP != null) dbSnp = new DbSnpBitSetUtil(DB_SNP, in.getFileHeader().getSequenceDictionary());
        else dbSnp = null;

        // Make an iterator that will filter out funny looking things
        final SamLocusIterator iterator;
        if (INTERVALS != null) {
            final IntervalList intervals = IntervalList.fromFile(INTERVALS);
            iterator = new SamLocusIterator(in, intervals.uniqued(), false);
        } else {
            iterator = new SamLocusIterator(in);
        }
        iterator.setEmitUncoveredLoci(false);
        iterator.setMappingQualityScoreCutoff(MINIMUM_MAPPING_QUALITY);
        iterator.setIncludeNonPfReads(INCLUDE_NON_PF_READS);

        final List<SamRecordFilter> filters = new ArrayList<>();
        filters.add(new NotPrimaryAlignmentFilter());
        filters.add(new DuplicateReadFilter());
        if (MINIMUM_INSERT_SIZE > 0 || MAXIMUM_INSERT_SIZE > 0) {
            filters.add(new InsertSizeFilter(MINIMUM_INSERT_SIZE, MAXIMUM_INSERT_SIZE));
        }
        iterator.setSamFilters(filters);

        log.info("Starting iteration.");
        long nextLogTime = 0;
        int sites = 0;

        for (final SamLocusIterator.LocusInfo info : iterator) {
            // Skip dbSNP sites
            final String chrom = info.getSequenceName();
            final int pos = info.getPosition();
            final int index = pos - 1;
            if (dbSnp != null && dbSnp.isDbSnpSite(chrom, pos)) continue;

            // Skip sites at the end of chromosomes 
            final byte[] bases = refWalker.get(info.getSequenceIndex()).getBases();
            if (pos <= CONTEXT_SIZE|| pos > bases.length - CONTEXT_SIZE) continue;

            // Skip non C-G bases
            final byte base = StringUtil.toUpperCase(bases[index]);
            if (base != 'C' && base != 'G') continue;

            // Get the context string
            final String context;
            {
                final String tmp = StringUtil.bytesToString(bases, index - CONTEXT_SIZE, 1 + (2 * CONTEXT_SIZE)).toUpperCase();
                if (base == 'C') context = tmp;
                else /* if G */  context = SequenceUtil.reverseComplement(tmp);
            }

            final List<Calculator> calculatorsForContext = calculators.get(context);
            if (calculatorsForContext == null) continue; // happens if we get ambiguous bases in the reference
            for (final Calculator calc : calculatorsForContext) calc.accept(info, base);

            // See if we need to stop
            if (++sites % 100 == 0) {
                final long now = System.currentTimeMillis();
                if (now > nextLogTime) {
                    log.info("Visited " + sites + " sites of interest. Last site: " + chrom + ":" + pos);
                    nextLogTime = now + 60000;
                }
            }
            if (sites >= STOP_AFTER) break;
        }

        final MetricsFile<CpcgMetrics, Integer> file = getMetricsFile();
        for (final List<Calculator> calcs : calculators.values()) {
            for (final Calculator calc : calcs) {
                final CpcgMetrics m = calc.finish();
                m.SAMPLE_ALIAS = StringUtil.join(",", new ArrayList<>(samples));
                file.addMetric(m);
            }
        }

        file.write(OUTPUT);
        CloserUtil.close(in);
        return 0;
    }

    private Set<String> makeContextStrings(final int contextSize) {
        final Set<String> contexts = new HashSet<>();

        for (final byte[] kmer : SequenceUtil.generateAllKmers(2 * contextSize + 1)) {
            if (kmer[contextSize] == 'C') {
                contexts.add(StringUtil.bytesToString(kmer));
            }
        }

        log.info("Generated " + contexts.size() + " context strings.");
        return contexts;
    }

    /** A little class for counting alleles. */
    private static class Counts {
        int controlA;
        int oxidatedA;
        int controlC;
        int oxidatedC;

        int total() { return controlC + oxidatedC + controlA + oxidatedA; }
    }

    /**
     * Class that calculated CpCG metrics for a specific library.
     */
    private class Calculator {
        private final String library;
        private final String context;

        // Things to be accumulated
        int sites = 0;
        long refCcontrolA = 0;
        long refCoxidatedA = 0;
        long refCcontrolC = 0;
        long refCoxidatedC = 0;
        long refGcontrolA = 0;
        long refGoxidatedA = 0;
        long refGcontrolC = 0;
        long refGoxidatedC = 0;

        Calculator(final String library, final String context) {
            this.library = library;
            this.context = context;
        }

        void accept(final SamLocusIterator.LocusInfo info, final byte refBase) {
            final Counts counts = computeAlleleFraction(info, refBase);

            if (counts.total() > 0) {
                // Things calculated on all sites with coverage
                this.sites++;
                if (refBase == 'C') {
                    this.refCcontrolA += counts.controlA;
                    this.refCoxidatedA += counts.oxidatedA;
                    this.refCcontrolC += counts.controlC;
                    this.refCoxidatedC += counts.oxidatedC;
                } else if (refBase == 'G') {
                    this.refGcontrolA += counts.controlA;
                    this.refGoxidatedA += counts.oxidatedA;
                    this.refGcontrolC += counts.controlC;
                    this.refGoxidatedC += counts.oxidatedC;
                } else {
                    throw new IllegalStateException("Reference bases other than G and C not supported.");
                }
            }
        }

        CpcgMetrics finish() {
            final CpcgMetrics m = new CpcgMetrics();
            m.LIBRARY = this.library;
            m.CONTEXT = this.context;
            m.TOTAL_SITES = this.sites;
            m.TOTAL_BASES = this.refCcontrolC + this.refCoxidatedC + this.refCcontrolA + this.refCoxidatedA +
                    this.refGcontrolC + this.refGoxidatedC + this.refGcontrolA + this.refGoxidatedA;
            m.REF_OXO_BASES = this.refCoxidatedC + refGoxidatedC;
            m.REF_NONOXO_BASES = this.refCcontrolC + this.refGcontrolC;
            m.REF_TOTAL_BASES = m.REF_OXO_BASES + m.REF_NONOXO_BASES;
            m.ALT_NONOXO_BASES = this.refCcontrolA + this.refGcontrolA;
            m.ALT_OXO_BASES = this.refCoxidatedA + this.refGoxidatedA;

            /**
             * Why do we calculate the oxo error rate using oxidatedA - controlA you ask?  We know that all the
             * bases counted in oxidatedA are consistent with 8-oxo-G damage during shearing, but not all of them
             * will have been caused by this. If we assume that C>A errors caused by other factors will occur randomly
             * with respect to read1/read2, then we should see as many in the 8-oxo-G consistent state as not.  So we
             * assume that controlA is half the story, and remove the other half from oxidatedA.
             */
            m.OXIDATION_ERROR_RATE = Math.max(m.ALT_OXO_BASES - m.ALT_NONOXO_BASES, 1) / (double) m.TOTAL_BASES;
            m.OXIDATION_Q = -10 * Math.log10(m.OXIDATION_ERROR_RATE);

            /** Now look for things that have a reference base bias! */
            m.C_REF_REF_BASES = this.refCcontrolC + this.refCoxidatedC;
            m.G_REF_REF_BASES = this.refGcontrolC + this.refGoxidatedC;
            m.C_REF_ALT_BASES = this.refCcontrolA + this.refCoxidatedA;
            m.G_REF_ALT_BASES = this.refGcontrolA + this.refGoxidatedA;

            final double cRefErrorRate = m.C_REF_ALT_BASES / (double) (m.C_REF_ALT_BASES + m.C_REF_REF_BASES);
            final double gRefErrorRate = m.G_REF_ALT_BASES / (double) (m.G_REF_ALT_BASES + m.G_REF_REF_BASES);

            m.C_REF_OXO_ERROR_RATE = Math.max(cRefErrorRate - gRefErrorRate, 1e-10);
            m.G_REF_OXO_ERROR_RATE = Math.max(gRefErrorRate - cRefErrorRate, 1e-10);
            m.C_REF_OXO_Q = -10 * Math.log10(m.C_REF_OXO_ERROR_RATE);
            m.G_REF_OXO_Q = -10 * Math.log10(m.G_REF_OXO_ERROR_RATE);

            return m;
        }

        /**
         *
         */
        private Counts computeAlleleFraction(final SamLocusIterator.LocusInfo info, final byte refBase) {
            final Counts counts = new Counts();
            final byte altBase = (refBase == 'C') ? (byte) 'A' : (byte) 'T';

            for (final SamLocusIterator.RecordAndOffset rec : info.getRecordAndOffsets()) {
                final byte qual;
                final SAMRecord samrec = rec.getRecord();

                if (USE_OQ) {
                    final byte[] oqs = samrec.getOriginalBaseQualities();
                    if (oqs != null) qual = oqs[rec.getOffset()];
                    else qual = rec.getBaseQuality();
                } else {
                    qual = rec.getBaseQuality();
                }

                // Skip if below qual, or if library isn't a match
                if (qual < MINIMUM_QUALITY_SCORE) continue;
                if (!this.library.equals(Optional.ofNullable(samrec.getReadGroup().getLibrary()).orElse(UNKNOWN_LIBRARY))) continue;

                // Get the read base, and get it in "as read" orientation
                final byte base = rec.getReadBase();
                final byte baseAsRead = samrec.getReadNegativeStrandFlag() ? SequenceUtil.complement(base) : base;
                final int read = samrec.getReadPairedFlag() && samrec.getSecondOfPairFlag() ? 2 : 1;

                // Figure out how to count the alternative allele. If the damage is caused by oxidation of G
                // during shearing (in non-rnaseq data), then we know that:
                //     G>T observation is always in read 1
                //     C>A observation is always in read 2
                // But if the substitution is from other causes the distribution of A/T across R1/R2 will be
                // random.
                if (base == refBase) {
                    if (baseAsRead == 'G' && read == 1) ++counts.oxidatedC;
                    else if (baseAsRead == 'G' && read == 2) ++counts.controlC;
                    else if (baseAsRead == 'C' && read == 1) ++counts.controlC;
                    else if (baseAsRead == 'C' && read == 2) ++counts.oxidatedC;
                } else if (base == altBase) {
                    if (baseAsRead == 'T' && read == 1) ++counts.oxidatedA;
                    else if (baseAsRead == 'T' && read == 2) ++counts.controlA;
                    else if (baseAsRead == 'A' && read == 1) ++counts.controlA;
                    else if (baseAsRead == 'A' && read == 2) ++counts.oxidatedA;
                }
            }

            return counts;
        }
    }
}
