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#include "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;
exit(1);
}
}
void SAMFullReadGroup::StoreValues(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;
}
}
}
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