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#include "ReferenceSequence.hpp"
const char* SAMReferenceSequence::SAMReferenceSequenceFieldNames[] = {"SN", "LN"};
void SAMReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, uint64_t lineNumber) {
(void)(lineNumber);
std::vector<bool> usedFields;
usedFields.resize(SQ_LN);
std::fill(usedFields.begin(), usedFields.end(), false);
for (size_t i = 0; i < kvPairs.size(); i++) {
if (kvPairs[i].key == "SN") {
sequenceName = kvPairs[i].value;
usedFields[SQ_SN] = true;
}
else if (kvPairs[i].key == "LN") {
StoreValue(kvPairs[i].value, length);
usedFields[SQ_SN] = true;
}
}
for (size_t i = 0; i < usedFields.size(); i++) {
if (usedFields[i] == false) {
std::cout << "SQ specifier missing " << SAMReferenceSequenceFieldNames[i] << std::endl;
}
}
}
const char* SAMFullReferenceSequence::SAMFullReferenceSequenceFieldNames[] = {"AS", "M5", "SP", "UR"};
void SAMFullReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
uint64_t lineNumber) {
SAMReferenceSequence::StoreValues(kvPairs, lineNumber);
for (size_t i = 0; i < kvPairs.size(); i++ ){
if (kvPairs[i].key == "AS") {
genomeAssembly = kvPairs[i].value;
}
else if (kvPairs[i].key == "M5") {
md5 = kvPairs[i].value;
}
else if (kvPairs[i].key == "SP") {
species = kvPairs[i].value;
}
else if (kvPairs[i].key == "UR") {
uri = kvPairs[i].value;
}
}
}
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