#include <pbdata/sam/SAMAlignment.hpp>

SAMAlignment::SAMAlignment()
{
    score = xs = xe = as = xt = xq = nm = fi = xl = 0;
    rg = optTagStr = "";
}

void SAMAlignment::PrintSAMAlignment(std::ostream& out)
{
    out << qName << "\t" << flag << "\t" << rName << "\t" << pos << "\t" << mapQV << "\t" << cigar
        << "\t" << rNext << "\t" << pNext << "\t" << tLen << "\t" << seq << "\t" << qual << "\t"
        << optTagStr << std::endl;
}

size_t SAMAlignment::FindPosOfNthChar(std::string str, int n, char c)
{
    if (n < 1) {
        std::cout << "Nth should be a positive integer." << std::endl;
        exit(EXIT_SUCCESS);
    }
    int count = 1;
    size_t pos = str.find(c, 0);
    // pos is the position of the first character c;
    while (count < n and pos != std::string::npos) {
        pos = str.find(c, pos + 1);
        count++;
    }
    return pos;
}

std::string SAMAlignment::TrimStringEnd(std::string str)
{
    std::string newStr = str;
    while (newStr[newStr.size() - 1] == '\r' or newStr[newStr.size() - 1] == '\n') {
        newStr.erase(newStr.size() - 1, 1);
    }
    return newStr;
}

bool SAMAlignment::StoreValues(std::string& line, int lineNumber)
{
    std::stringstream strm(line);
    std::vector<bool> usedFields;
    usedFields.resize(S_QUAL);
    std::fill(usedFields.begin(), usedFields.end(), false);
    std::string kvPair;
    bool parseError = false;
    SAMAlignmentRequiredFields field{};
    //
    // Define a temporary mapqv value that gets over a GMAP bug that prints a mapqv < 0.
    //
    int tmpMapQV = 0;
    if (!(strm >> qName)) {
        parseError = true;
        field = S_QNAME;
    } else if (!(strm >> flag)) {
        parseError = true;
        field = S_FLAG;
    } else if (!(strm >> rName)) {
        parseError = true;
        field = S_RNAME;
    } else if (!(strm >> pos)) {
        parseError = true;
        field = S_POS;
    } else if (!(strm >> tmpMapQV)) {
        parseError = true;
        field = S_MAPQV;
    } else if (!(strm >> cigar)) {
        parseError = true;
        field = S_CIGAR;
    }

    else if (!(strm >> rNext)) {
        parseError = true;
        field = S_RNEXT;
    }

    else if (!(strm >> pNext)) {
        parseError = true;
        field = S_PNEXT;
    } else if (!(strm >> tLen)) {
        parseError = true;
        field = S_TLEN;
    } else if (!(strm >> seq)) {
        parseError = true;
        field = S_SEQ;
    } else if (!(strm >> qual)) {
        parseError = true;
        field = S_QUAL;
    }

    mapQV = (unsigned char)tmpMapQV;

    // Find posisition of the 11th tab.
    size_t optTagsStartPos = FindPosOfNthChar(strm.str(), 11, '\t');
    // Save all optional tags.
    if (optTagsStartPos != std::string::npos) {
        optTagStr = strm.str().substr(optTagsStartPos + 1);
        optTagStr = TrimStringEnd(optTagStr);
    }

    //
    // If not aligned, stop trying to read in elements from the sam string.
    //
    if (rName == "*") {
        return true;
    }

    if (parseError) {
        std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field "
                  << SAMAlignmentRequiredFieldNames[field] << std::endl;
        std::exit(EXIT_FAILURE);
    }

    //
    // Now parse optional data.
    //
    while (strm) {
        std::string kvName, kvType, kvValue;
        std::string typedKVPair;
        if (!(strm >> typedKVPair)) {
            break;
        }
        if (TypedKeywordValuePair::Separate(typedKVPair, kvName, kvType, kvValue)) {
            std::stringstream strm(kvValue);
            if (kvName == "RG") {
                rg = kvValue;
            } else if (kvName == "AS") {
                strm >> as;
            } else if (kvName == "XS") {
                strm >> xs;
            } else if (kvName == "XE") {
                strm >> xe;
            } else if (kvName == "XL") {
                strm >> xl;
            } else if (kvName == "XT") {
                strm >> xt;
            } else if (kvName == "NM") {
                strm >> nm;
            } else if (kvName == "FI") {
                strm >> fi;
            } else if (kvName == "XQ") {
                strm >> xq;
            }  // Add quality values, including QualityValue?,
               // InsertionQV, DeletionQV, SubstitutionQV,
               // MergeQV and SubstitutionTag and DeletionTag
            else if (kvName == "iq") {
                strm >> iq;
            } else if (kvName == "dq") {
                strm >> dq;
            } else if (kvName == "sq") {
                strm >> sq;
            } else if (kvName == "mq") {
                strm >> mq;
            } else if (kvName == "st") {
                strm >> st;
            } else if (kvName == "dt") {
                strm >> dt;
            }
        } else {
            std::cout << "ERROR. Could not parse typed keyword value " << typedKVPair << std::endl;
            exit(EXIT_SUCCESS);
        }
    }
    return true;
}

void SAMAlignment::CopyQVs(std::vector<std::string>* optionalQVs)
{
    optionalQVs->clear();
    optionalQVs->push_back(iq);
    optionalQVs->push_back(dq);
    optionalQVs->push_back(sq);
    optionalQVs->push_back(mq);
    optionalQVs->push_back(st);
    optionalQVs->push_back(dt);
}

const char* SAMAlignment::SAMAlignmentRequiredFieldNames[] = {
    "QNAME", "FLAG", "RNAME", "POS", "MAPQV", "CIGAR", "RNEXT", "PNEXT", "TLEN", "SEQ", "QUAL"};
const char* optionalQVTags[] = {"iq", "dq", "sq", "mq", "st", "dt"};
const char* optionalQVNames[] = {"InsertionQV", "DeletionQV",      "SubstitutionQV",
                                 "MergeQV",     "SubstitutionTag", "DeletionTag"};