#include "ParametersSolo.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include "SequenceFuns.h"
#include "serviceFuns.cpp"

#include <stdlib.h>

const vector<string> ParametersSolo::featureNames={"Gene","SJ"};

void ParametersSolo::initialize(Parameters *pPin) 
{
    pP=pPin;
    
    if (typeStr=="None") {
        type=0;
        return;
    } else if (typeStr=="Droplet") {
        type=1;
        bL=cbL+umiL;
        pP->readNmates=1; //output mates TODO: check that readNmatesIn==2
    } else  {
        ostringstream errOut;
        errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloType="<<typeStr<<"\n";
        errOut << "SOLUTION: use allowed option: None or Droplet";
        exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
    }; 
    
    if (strandStr=="Unstranded") {
        strand=-1;
    } else if (strandStr=="Forward") {
        strand=0;
    } else if (strandStr=="Reverse") {
        strand=1;        
    } else  {
        ostringstream errOut;
        errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloStrand="<<strandStr<<"\n";
        errOut << "SOLUTION: use allowed option: Unstranded OR Forward OR Reverse";
        exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
    };
    
    for (auto &fin : featureIn) {
        bool finGood=false;
        for (uint32 ii=0; ii<featureNames.size(); ii++) {
            if (fin==featureNames[ii]) {
                finGood=true;
                featureYes[ii]=true;
                features.push_back(ii);
                break;
            };
        };
        if (!finGood) {
            ostringstream errOut;
            errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloFeatures="<<fin<<"\n";
            errOut << "SOLUTION: use allowed option: ";
            errOut <<featureNames[0]<< "   OR   ";            
            for (auto &fname : featureNames)
                errOut << fname <<" ";
            exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
        };
    };
    nFeatures=features.size();
    
    umiDedupYes.resize(3,false);
    umiDedupColumns.resize(umiDedup.size());
    for (uint32 ii=0; ii<umiDedup.size(); ii++) {
        if (umiDedup[ii]=="1MM_NotCollapsed") {
            umiDedupYes[0]=true; 
            umiDedupColumns[ii]=0;
        } else if (umiDedup[ii]=="1MM_All") {
            umiDedupYes[1]=true;
            umiDedupColumns[ii]=1;            
        } else if (umiDedup[ii]=="1MM_Directional") {
            umiDedupYes[2]=true;
            umiDedupColumns[ii]=2;
        } else {
            ostringstream errOut;
            errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloUMIdedup="<<umiDedup[ii]<<"\n";
            exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);            
        };
    };
    ///////////// finished parameters input
    
    //make output directory if needed
    if ( outFileNames[0].find_last_of("/") < outFileNames[0].size() ) {//need to create dir
        string dir1=pP->outFileNamePrefix+outFileNames[0].substr(0,outFileNames[0].find_last_of("/"));
        if (mkdir(dir1.c_str(),pP->runDirPerm)!=0 && errno!=EEXIST) {
            ostringstream errOut;
            errOut << "EXITING because of fatal OUTPUT FILE error: could not create Solo output directory"<<dir1<<"\n";
            errOut << "SOLUTION: check the path and permisssions";
            exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
        };
    };
    
    QSbase=33;//TODO make these user-definable
    QSmax=33;
    cbMinP=0.975;
    
    umiMaskLow=(uint32) ( (((uint64)1)<<umiL) - 1);
    umiMaskHigh=~umiMaskLow;
    
    //load the CB whitlist and create unordered_map
    ifstream & cbWlStream = ifstrOpen(soloCBwhitelist, ERROR_OUT, "SOLUTION: check the path and permissions of the CB whitelist file: " + soloCBwhitelist, *pP);
    string seq1;
    while (cbWlStream >> seq1) {
        if (seq1.size() != cbL) {
            ostringstream errOut;
            errOut << "EXITING because of FATAL ERROR in input CB whitelist file: "<< soloCBwhitelist <<" the total length of barcode sequence is "  << seq1.size() << " not equal to expected " <<bL <<"\n"  ;
            errOut << "SOLUTION: make sure that the barcode read is the second in --readFilesIn and check that is has the correct formatting\n";
            exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
        };
        uint32 cb1;
        //convert to 2-bit format
        if (convertNuclStrToInt32(seq1,cb1)) {
            //cbWL.insert(cb1);
            cbWL.push_back(cb1);
        } else {
            pP->inOut->logMain << "WARNING: CB whitelist sequence contains non-ACGT and is ignored: " << seq1 <<endl;
        };
    };
    //int comp1 = [] (const void *a, const void *b) {uint32 aa=*(uint32*) a; uint32 bb=*(uint32*) b; if (a 
    qsort(cbWL.data(),cbWL.size(),sizeof(uint32),funCompareNumbers<uint32>);
    
    if (!pP->quant.trSAM.yes) {
        pP->quant.yes = true;
        pP->quant.trSAM.yes = true;
        pP->quant.trSAM.bamYes = false;
        pP->quant.trSAM.bamCompression = -2;
        pP->quant.trSAM.indel = true;
        pP->quant.trSAM.softClip = true;
        pP->inOut->logMain << "Turning on Genomic->Transcriptomic coordinate conversion for STARsolo\n";
    };

    time_t rawTime;
    time(&rawTime);
    pP->inOut->logMain << timeMonthDayTime(rawTime) << "Finished reading CB whitelist sequences: " << cbWL.size() <<endl;
};