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#include <hdf/HDFCmpExperimentGroup.hpp>
#include <iostream>
bool HDFCmpExperimentGroup::Create(HDFGroup &parent, std::string experimentGroupName)
{
parent.AddGroup(experimentGroupName);
if (experimentGroup.Initialize(parent.group, experimentGroupName) == 0) {
return 0;
}
alignmentArray.Create(experimentGroup, "AlnArray");
return true;
}
void HDFCmpExperimentGroup::AddAlignment(std::vector<unsigned char> &alignment,
unsigned int &offsetBegin, unsigned int &offsetEnd)
{
offsetBegin = offsetEnd = 0;
if (alignment.size() == 0) {
//
// Do not increment anything.
//
return;
}
// Make a copy of alignment.
std::vector<unsigned char> paddedAlignment = alignment;
// Pad '0' to the end of the alignment.
paddedAlignment.push_back(0);
offsetBegin = alignmentArray.size(); // 0 based, inclusive
offsetEnd = offsetBegin + alignment.size(); // 0 based, exclusive
// alignmentArray[offsetEnd] is not a part of the real alignment, it is the padded 0.
alignmentArray.Write(&paddedAlignment[0], paddedAlignment.size());
}
//template<typename T>
//void HDFCmpExperimentGroup::AddQualityValues(const std::vector<T> &qualityValues,
// const std::string &fieldName,
// unsigned int *offsetBegin,
// unsigned int *offsetEnd) {
//
// std::vector<T> paddedQualityValues = qualityValues;
// paddedQualityValues.push_back(0);
// HDFArray<T> *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 if (fieldName == "DeletionTag") {
// arrayPtr = &deletionTag;
// } else if (fieldName == "SubstitutionTag") {
// arrayPtr = &substitutionTag;
// } else {
// assert(false);
// }
//
// *offsetBegin = arrayPtr->size();
// *offsetEnd = arrayPtr->size() + qualityValues.size();
//
// arrayPtr->Write(&paddedQualityValues[0], paddedQualityValues.size());
//}
//
//// One for tags, one for QVs
//template void HDFCmpExperimentGroup::AddQualityValues<char>(
// const std::vector<char>&, const std::string&,
// unsigned int*, unsigned int*);
//
//template void HDFCmpExperimentGroup::AddQualityValues<UChar>(
// const std::vector<UChar>&, const std::string&,
// unsigned int*, unsigned int*);
//
int HDFCmpExperimentGroup::Initialize(HDFGroup &refGroup, std::string experimentGroupName,
std::set<std::string> &fieldNames)
{
//
// Normal initialization that prepares for reading alignments
//
Initialize(refGroup, experimentGroupName);
//
// Field initialization for reading in pulse/quality information.
//
std::set<std::string>::iterator fieldNameIt, fieldEnd;
fieldEnd = fieldNames.end();
for (fieldNameIt = fieldNames.begin(); fieldNameIt != fieldEnd; ++fieldNameIt) {
if (supportedFields.find(*fieldNameIt) != supportedFields.end() and
experimentGroup.ContainsObject(*fieldNameIt)) {
fields[*fieldNameIt]->Initialize(experimentGroup, *fieldNameIt);
} else {
std::cout << "Unable to initialize requested field " << *fieldNameIt
<< " in experiment group " << experimentGroupName << std::endl;
}
}
return 1;
}
int HDFCmpExperimentGroup::Initialize(HDFGroup &refGroup, std::string experimentGroupName)
{
if (experimentGroup.Initialize(refGroup.group, experimentGroupName) == 0) {
return 0;
}
if (alignmentArray.Initialize(experimentGroup, "AlnArray") == 0) {
return 0;
}
return 1;
}
HDFCmpExperimentGroup::HDFCmpExperimentGroup()
{
fields["StartTimeOffset"] = &this->startTimeOffset;
fields["QualityValue"] = &this->qualityValue;
fields["IPD"] = &this->ipd;
fields["PreBaseFrames"] = &this->preBaseFrames;
fields["DeletionQV"] = &this->deletionQV;
fields["InsertionQV"] = &this->insertionQV;
fields["ClassifierQV"] = &this->classifierQV;
fields["SubstitutionQV"] = &this->substitutionQV;
fields["Light"] = &this->light;
fields["WidthInFrames"] = &this->widthInFrames;
fields["PulseWidth"] = &this->pulseWidth;
fields["StartFrame"] = &this->startTime;
// StartFrame computed from Pulse metrics and Base metrics
fields["StartFramePulse"] = &this->startTimePulse;
fields["StartFrameBase"] = &this->startTimeBase;
fields["pkmid"] = &this->pkmid;
fields["pkmax"] = &this->pkmax;
fields["pkmean"] = &this->pkmean;
fields["DeletionTag"] = &this->deletionTag;
fields["SubstitutionTag"] = &this->substitutionTag;
fields["PulseIndex"] = &this->pulseIndex;
fields["MergeQV"] = &this->mergeQV;
}
// Return reference alignment AlnArray size in KB.
UInt HDFCmpExperimentGroup::GetAlnArraySize()
{
return alignmentArray.arrayLength / 1024 * sizeof(unsigned char);
}
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());
}
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