#include <pbdata/sam/ReadGroup.hpp>

void SAMReadGroup::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, uint64_t lineNumber)
{
    bool idIsStored = false;
    for (size_t i = 0; i < kvPairs.size(); i++) {
        if (kvPairs[i].key == "ID") {
            id = kvPairs[i].value;
            idIsStored = true;
        }
    }
    if (idIsStored == false) {
        std::cout << "ReadGroup missing id at " << lineNumber << std::endl;
        std::exit(EXIT_FAILURE);
    }
}

void SAMFullReadGroup::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, uint64_t lineNumber)
{
    SAMReadGroup::StoreValues(kvPairs, lineNumber);
    std::string kwPair;
    std::string key, valueStr;
    for (size_t i = 0; i < kvPairs.size(); i++) {
        if (kvPairs[i].key == "CN") {
            centerName = kvPairs[i].value;
        } else if (kvPairs[i].key == "DS") {
            description = kvPairs[i].value;
        } else if (kvPairs[i].key == "DT") {
            date = kvPairs[i].value;
        } else if (kvPairs[i].key == "FO") {
            flowOrder = kvPairs[i].value;
        } else if (kvPairs[i].key == "LB") {
            library = kvPairs[i].value;
        } else if (kvPairs[i].key == "PG") {
            processingProgram = kvPairs[i].value;
        } else if (kvPairs[i].key == "PI") {
            StoreValue(kvPairs[i].value, insertSize);
        } else if (kvPairs[i].key == "SM") {
            sample = kvPairs[i].value;
        }
    }
}