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// Author: Yuan Li
#include <hdf/HDFZMWMetricsWriter.hpp>
#include <pbdata/reads/ScanData.hpp>
HDFZMWMetricsWriter::HDFZMWMetricsWriter(const std::string& filename, HDFGroup& parentGroup,
const std::map<char, size_t>& baseMap)
: HDFWriterBase(filename), parentGroup_(parentGroup), baseMap_(baseMap), curRow_(0)
{
if (not parentGroup.groupIsInitialized)
PARENT_GROUP_NOT_INITIALIZED_ERROR(PacBio::GroupNames::zmwmetrics);
else {
parentGroup_.AddGroup(PacBio::GroupNames::zmwmetrics);
if (zmwMetricsGroup_.Initialize(parentGroup_, PacBio::GroupNames::zmwmetrics) == 0)
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::zmwmetrics);
InitializeChildHDFGroups();
}
// Sanity Check BaseMap
assert(ScanData::IsValidBaseMap(baseMap));
}
HDFZMWMetricsWriter::~HDFZMWMetricsWriter()
{
Flush(); // Must flush in case group is empty.
assert(WriteAttributes());
Close();
}
bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence& read)
{
try {
float snrs[4];
for (char base : {'A', 'C', 'G', 'T'}) {
snrs[baseMap_[base]] = read.HQRegionSnr(base);
}
hqRegionSNRArray_.WriteRow(snrs, SNRNCOLS);
readScoreArray_.Write(&read.readScore, 1);
productivityArray_.Write(&read.zmwData.holeStatus, 1);
} catch (H5::Exception& e) {
AddErrorMessage("Failed to write HQRegionSNR or ReadScore or Productivity.");
return false;
}
++curRow_;
return true;
}
void HDFZMWMetricsWriter::Flush(void)
{
hqRegionSNRArray_.Flush();
readScoreArray_.Flush();
productivityArray_.Flush();
}
void HDFZMWMetricsWriter::Close(void)
{
hqRegionSNRArray_.Close();
readScoreArray_.Close();
productivityArray_.Close();
zmwMetricsGroup_.Close();
}
bool HDFZMWMetricsWriter::InitializeChildHDFGroups(void)
{
bool OK = true;
if (hqRegionSNRArray_.Initialize(zmwMetricsGroup_, PacBio::GroupNames::hqregionsnr, SNRNCOLS) ==
0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::hqregionsnr);
OK = false;
}
if (readScoreArray_.Initialize(zmwMetricsGroup_, PacBio::GroupNames::readscore) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::readscore);
OK = false;
}
if (productivityArray_.Initialize(zmwMetricsGroup_, PacBio::GroupNames::productivity) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::productivity);
OK = false;
}
return OK;
}
bool HDFZMWMetricsWriter::WriteAttributes(void)
{
if (curRow_ > 0) {
bool OK = AddAttribute<std::string>(
hqRegionSNRArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMWMetrics::HQRegionSNR::description) and
AddAttribute<std::string>(
readScoreArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMWMetrics::ReadScore::description) and
AddAttribute<std::string>(
productivityArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMWMetrics::Productivity::description);
return OK;
} else {
AddErrorMessage("Could not write attributes when ZMWMetrics group is empty.");
return false;
}
}
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