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

import htsjdk.samtools.*;
import org.broadinstitute.gatk.engine.io.NWaySAMFileWriter;
import org.broadinstitute.gatk.utils.commandline.Advanced;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Hidden;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter;
import org.broadinstitute.gatk.engine.iterators.RNAReadTransformer;
import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.DataSource;
import org.broadinstitute.gatk.engine.walkers.ReadWalker;
import org.broadinstitute.gatk.engine.walkers.Requires;
import org.broadinstitute.gatk.utils.clipping.ReadClipper;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.sam.CigarUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;

import java.io.FileNotFoundException;
import java.util.Collections;
import java.util.List;
import java.util.ArrayList;

/**
 *
 * Splits reads that contain Ns in their CIGAR string
 *
 * <p>This tool identifies all N cigar elements in sequence reads, and creates k+1 new reads
 * (where k is the number of N cigar elements) that correspond to the segments of the original read beside/between
 * the splicing events represented by the Ns in the original CIGAR. The first read includes the bases that are to the
 * left of the first N element, while the part of the read that is to the right of the N (including the Ns) is hard
 * clipped, and so on for the rest of the new reads.</p>
 *
 * <h3>Input</h3>
 * <p>
 * One or more bam files.
 * </p>
 *
 * <h3>Output</h3>
 * <p>
 * A single processed bam file.
 * </p>
 *
 * <h3>Usage example</h3>
 * <pre>
 * java -jar GenomeAnalysisTK.jar \
 *   -T SplitNCigarReads \
 *   -R reference.fasta \
 *   -I input.bam \
 *   -o output.bam \
 *   -U ALLOW_N_CIGARS
 *
 * <h3>Note</h3>
 * <p>When this tool is used as part of the RNAseq best practices, the command should include mapping quality
 * reassignment. See the Best Practices documentation for details.</p>
 *
 */

@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS, DataSource.REFERENCE})
public class SplitNCigarReads extends ReadWalker<GATKSAMRecord, OverhangFixingManager> {

    // The name that will go in the @PG tag
    public static final String PROGRAM_RECORD_NAME = "GATK SplitNCigarReads";


    @Output(doc="Write output to this BAM filename instead of STDOUT")
    protected GATKSAMFileWriter writer;

    /**
     * For expert users only!  To minimize memory consumption you can lower this number, but then the tool may skip
     * overhang fixing in regions with too much coverage.  Just make sure to give Java enough memory!  4Gb should be
     * enough with the default value.
     */
    @Advanced
    @Argument(fullName="maxReadsInMemory", shortName="maxInMemory", doc="max reads allowed to be kept in memory at a time by the BAM writer", required=false)
    protected int MAX_RECORDS_IN_MEMORY = 150000;

    /**
     * If there are more than this many mismatches within the overhang regions, the whole overhang will get hard-clipped out.
     * It is still possible in some cases that the overhang could get clipped if the number of mismatches do not exceed this
     * value, e.g. if most of the overhang mismatches.
     */
    @Advanced
    @Argument(fullName="maxMismatchesInOverhang", shortName="maxMismatches", doc="max number of mismatches allowed in the overhang", required=false)
    protected int MAX_MISMATCHES_IN_OVERHANG = 1;

    /**
     * If there are more than this many bases in the overhang, we won't try to hard-clip them out
     */
    @Advanced
    @Argument(fullName="maxBasesInOverhang", shortName="maxOverhang", doc="max number of bases allowed in the overhang", required=false)
    protected int MAX_BASES_TO_CLIP = 40;

    @Argument(fullName="doNotFixOverhangs", shortName="doNotFixOverhangs", doc="do not have the walker hard-clip overhanging sections of the reads", required=false)
    protected boolean doNotFixOverhangs = false;

    @Hidden
    @Argument(fullName = "no_pg_tag", shortName = "npt", doc = "Necessary for integration tests", required = false)
    protected boolean NO_PG_TAG = false;

    /**
     * This stores all of the already-split reads and manages any processing (e.g. clipping overhangs) that happens to them.
     * It will emit reads to the underlying writer as needed so we don't need to worry about any of that in this class.
     */
    protected OverhangFixingManager overhangManager;
    private List<RNAReadTransformer> rnaReadTransformers = new ArrayList<>();


    @Override
    public void initialize() {
        final GenomeAnalysisEngine toolkit = getToolkit();

        if ( getToolkit() != null ) {
            for (final ReadTransformer transformer: getToolkit().getReadTransformers())
                if(transformer instanceof RNAReadTransformer)                     // TODO: when a read transformer can be called directly from the command line we won't need that mechanism any more
                    rnaReadTransformers.add((RNAReadTransformer)transformer);
        }
        if ( !NO_PG_TAG ) {
            // we don't want to assume that reads will be written in order by the manager because in deep, deep pileups it won't work
            NWaySAMFileWriter.setupWriter(writer, toolkit, toolkit.getSAMFileHeader(), false, this, PROGRAM_RECORD_NAME);
        }

        try {
            final CachingIndexedFastaSequenceFile referenceReader = new CachingIndexedFastaSequenceFile(toolkit.getArguments().referenceFile);
            overhangManager = new OverhangFixingManager(writer, toolkit.getGenomeLocParser(), referenceReader, MAX_RECORDS_IN_MEMORY, MAX_MISMATCHES_IN_OVERHANG, MAX_BASES_TO_CLIP, doNotFixOverhangs);
        }
        catch (FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(toolkit.getArguments().referenceFile, ex);
        }
    }

    @Override
    public GATKSAMRecord map(final ReferenceContext ref, final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker) {
        GATKSAMRecord workingRead = read;

        for ( final RNAReadTransformer transformer : rnaReadTransformers ) {
            workingRead = transformer.apply(workingRead);                    // TODO: when a read transformer can be called directly from the command line we won't need that mechanism any more
        }

        return workingRead;
    }

    @Override
    public OverhangFixingManager reduceInit() {
        return overhangManager;
    }

    @Override
    public OverhangFixingManager reduce(final GATKSAMRecord read, final OverhangFixingManager manager) {
        splitNCigarRead(read, manager);
        return manager;
    }

    @Override
    public void onTraversalDone(final OverhangFixingManager manager) {
        manager.close();
    }

    /**
     * Goes through the cigar string of the read and create new reads for each consecutive non-N elements (while hard clipping the rest of the read).
     * For example: for a read with cigar '1H2M2D1M2N1M2I1N1M2S' 3 new reads will be created with cigar strings: 1H2M2D1M, 1M2I and 1M2S
     *
     * @param read     the read to split
     * @param manager  the output manager
     */
    public static void splitNCigarRead(final GATKSAMRecord read, final OverhangFixingManager manager) {
        final int numCigarElements = read.getCigar().numCigarElements();

        int firstCigarIndex = 0;
        for ( int i = 0; i < numCigarElements; i++ ) {
            final CigarElement cigarElement = read.getCigar().getCigarElement(i);
            if (cigarElement.getOperator() == CigarOperator.N) {
                manager.addRead(splitReadBasedOnCigar(read, firstCigarIndex, i, manager));
                firstCigarIndex = i+1;
            }
        }

        // if there are no N's in the read
        if (firstCigarIndex == 0) {
            manager.addRead(read);
        }
        //add the last section of the read: from the last N to the the end of the read
        // (it will be done for all the usual cigar string that does not end with N)
        else if (firstCigarIndex < numCigarElements) {
            manager.addRead(splitReadBasedOnCigar(read, firstCigarIndex, numCigarElements, null));
        }
    }

    /**
     * Pull out an individual split position for a read
     *
     * @param read               the read being split
     * @param cigarStartIndex    the index of the first cigar element to keep
     * @param cigarEndIndex      the index of the last cigar element to keep
     * @param forSplitPositions  the manager for keeping track of split positions; can be null
     * @return a non-null read representing the section of the original read being split out
     */
    private static GATKSAMRecord splitReadBasedOnCigar(final GATKSAMRecord read, final int cigarStartIndex, final int cigarEndIndex, final OverhangFixingManager forSplitPositions) {
        int cigarFirstIndex = cigarStartIndex;
        int cigarSecondIndex = cigarEndIndex;

        //in case a section of the read ends or starts with D (for example the first section in 1M1D1N1M is 1M1D), we should trim this cigar element
        // it can be 'if', but it was kept as 'while' to make sure the code can work with Cigar strings that were not "cleaned"
        while(read.getCigar().getCigarElement(cigarFirstIndex).getOperator().equals(CigarOperator.D))
            cigarFirstIndex++;
        while(read.getCigar().getCigarElement(cigarSecondIndex-1).getOperator().equals(CigarOperator.D))
            cigarSecondIndex--;
        if(cigarFirstIndex > cigarSecondIndex)
            throw new UserException.BadInput("Cannot split this read (might be an empty section between Ns, for example 1N1D1N): "+read.getCigarString());

        // we keep only the section of the read that is aligned to the reference between startRefIndex and stopRefIndex (inclusive).
        // the other sections of the read are clipped:
        final int startRefIndex = read.getOriginalAlignmentStart() + CigarUtils.countRefBasesBasedOnCigar(read,0,cigarFirstIndex); //goes through the prefix of the cigar (up to cigarStartIndex) and move the reference index.
        final int stopRefIndex = startRefIndex + CigarUtils.countRefBasesBasedOnCigar(read,cigarFirstIndex,cigarSecondIndex)-1; //goes through a consecutive non-N section of the cigar (up to cigarEndIndex) and move the reference index.

        if ( forSplitPositions != null ) {
            final String contig = read.getReferenceName();
            final int splitStart = startRefIndex + CigarUtils.countRefBasesBasedOnCigar(read,cigarFirstIndex,cigarEndIndex);  //we use cigarEndIndex instead of cigarSecondIndex so we won't take into account the D's at the end.
            final int splitEnd = splitStart + read.getCigar().getCigarElement(cigarEndIndex).getLength() - 1;
            forSplitPositions.addSplicePosition(contig, splitStart, splitEnd);
        }

        return ReadClipper.hardClipToRegionIncludingClippedBases(read, startRefIndex, stopRefIndex);
    }
}
