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#include <pbdata/sam/SAMHeader.hpp>
#include <algorithm>
void SAMHeader::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, int lineNumber)
{
for (size_t i = 0; i < kvPairs.size(); i++) {
if (kvPairs[i].key == "VN") {
formatVersion = kvPairs[i].value;
} else if (kvPairs[i].key == "SO") {
std::string value = kvPairs[i].value;
std::transform(value.begin(), value.end(), value.begin(), ::tolower);
if (value == "unknown" || value == "unsorted") {
sortingOrder = unknown;
} else if (value == "sorted") {
sortingOrder = sorted;
} else if (value == "queryname") {
sortingOrder = queryname;
} else if (value == "coordinate") {
sortingOrder = coordinate;
} else {
std::cout << "Invalid sorting order " << kvPairs[i].value << " at line "
<< lineNumber;
}
}
}
}
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