void HDFCmpExperimentGroup::AddQVs(const std::vector<UChar> &qualityValues,
const std::string &fieldName, unsigned int *offsetBegin,
unsigned int *offsetEnd)
{
std::vector<UChar> paddedQualityValues = qualityValues;
paddedQualityValues.push_back(0);
HDFArray<UChar> *arrayPtr = NULL;
// This seems to be how we do it
if (fieldName == "DeletionQV") {
arrayPtr = &deletionQV;
} else if (fieldName == "InsertionQV") {
arrayPtr = &insertionQV;
} else if (fieldName == "MergeQV") {
arrayPtr = &mergeQV;
} else if (fieldName == "SubstitutionQV") {
arrayPtr = &substitutionQV;
} else {
assert(false);
}
if (!arrayPtr->isInitialized) arrayPtr->Initialize(experimentGroup, fieldName);
*offsetBegin = arrayPtr->size();
*offsetEnd = arrayPtr->size() + qualityValues.size();
arrayPtr->Write(&paddedQualityValues[0], paddedQualityValues.size());
}
void HDFCmpExperimentGroup::AddTags(const std::vector<char> &qualityValues,
const std::string &fieldName, unsigned int *offsetBegin,
unsigned int *offsetEnd)
{
std::vector<char> paddedQualityValues = qualityValues;
paddedQualityValues.push_back(0);
HDFArray<char> *arrayPtr = NULL;
if (fieldName == "DeletionTag") {
arrayPtr = &deletionTag;
} else if (fieldName == "SubstitutionTag") {
arrayPtr = &substitutionTag;
} else {
assert(false);
}
if (!arrayPtr->isInitialized) arrayPtr->Initialize(experimentGroup, fieldName);
*offsetBegin = arrayPtr->size();
*offsetEnd = arrayPtr->size() + qualityValues.size();
arrayPtr->Write(&paddedQualityValues[0], paddedQualityValues.size());
}