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#include <LibBlasrConfig.h>
#ifdef USE_PBBAM
#include <hdf/HDFZMWWriter.hpp>
HDFZMWWriter::HDFZMWWriter(const std::string& filename, HDFGroup& parentGroup,
const bool inPulseCalls, const std::map<char, size_t>& baseMap)
: HDFWriterBase(filename)
, parentGroup_(parentGroup)
, baseMap_(baseMap)
, inPulseCalls_(inPulseCalls)
, arrayLength_(0)
{
if (not parentGroup.groupIsInitialized)
PARENT_GROUP_NOT_INITIALIZED_ERROR(PacBio::GroupNames::zmw);
else {
parentGroup_.AddGroup(PacBio::GroupNames::zmw);
if (zmwGroup_.Initialize(parentGroup_, PacBio::GroupNames::zmw) == 0)
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::zmw);
this->InitializeChildHDFGroups();
}
}
HDFZMWWriter::HDFZMWWriter(const std::string& filename, HDFGroup& parentGroup)
: HDFZMWWriter(filename, parentGroup, false, {})
{
}
HDFZMWWriter::~HDFZMWWriter(void)
{
this->_WriteAttributes();
this->Close();
}
bool HDFZMWWriter::InPulseCalls(void) const { return inPulseCalls_; }
bool HDFZMWWriter::HasBaseLineSigma(void) const
{
return false; // base line sigma won't be provided util 3.0.1 bug 29486
//return InPulseCalls() and baseLineSigmaArray_.IsInitialized();
}
bool HDFZMWWriter::WriteOneZmw(const SMRTSequence& read)
{
_WriteNumEvent(read.length);
_WriteHoleNumber(read.HoleNumber());
_WriteHoleXY(static_cast<int16_t>(read.HoleX()), static_cast<int16_t>(read.HoleY()));
_WriteHoleStatus(read.HoleStatus());
arrayLength_++;
return Errors().empty();
}
bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord& read)
{
if (InPulseCalls()) {
if (not read.HasPulseCall()) {
AddErrorMessage(std::string("PulseCall absent in read ") + read.FullName());
} else {
_WriteNumEvent(read.PulseCall().size());
}
} else {
_WriteNumEvent(read.Sequence().size());
}
arrayLength_++;
uint32_t hn_ = read.HoleNumber();
_WriteHoleNumber(hn_);
_WriteHoleXY(static_cast<int16_t>(hn_ >> 16), static_cast<int16_t>(hn_ & 0x0000FFFF));
_WriteHoleStatus(PacBio::AttributeValues::ZMW::HoleStatus::sequencingzmw);
_WriteBaseLineSigma(read);
return Errors().empty();
}
bool HDFZMWWriter::WriteFakeDataSets(void)
{
// Fake BaselineLevel, BaselineSigma, SignalLevel, SignalSigma
//std::vector<float> buffer(arrayLength_);
//std::fill(buffer.begin(), buffer.end(), 0.0);
return __WriteFake2DDataSet<float>(zmwGroup_, PacBio::GroupNames::baselinelevel, arrayLength_,
4, 0) and
__WriteFake2DDataSet<float>(zmwGroup_, PacBio::GroupNames::baselinesigma, arrayLength_,
4, 0) and
__WriteFake2DDataSet<float>(zmwGroup_, PacBio::GroupNames::signallevel, arrayLength_, 4,
0) and
__WriteFake2DDataSet<float>(zmwGroup_, PacBio::GroupNames::signalsigma, arrayLength_, 4,
0);
}
bool HDFZMWWriter::_WriteNumEvent(const uint32_t numEvent)
{
numEventArray_.Write(&numEvent, 1);
return true;
}
bool HDFZMWWriter::_WriteHoleNumber(const uint32_t holeNumber)
{
holeNumberArray_.Write(&holeNumber, 1);
return true;
}
bool HDFZMWWriter::_WriteHoleXY(const int16_t holeX, const int16_t holeY)
{
int16_t xy[2] = {holeX, holeY};
holeXYArray_.WriteRow(xy, 2);
return true;
}
bool HDFZMWWriter::_WriteHoleStatus(const unsigned char holeStatus)
{
// NOTE that: We assume that all zmws in BAM are SEQUENCING zmws.
holeStatusArray_.Write(&holeStatus, 1);
return true;
}
bool HDFZMWWriter::_WriteBaseLineSigma(const PacBio::BAM::BamRecord& read)
{
// FIXME: pbbam should provide APIs: HasBaseLineSigma and BaseLineSigma().
if (HasBaseLineSigma()) {
if (read.Impl().HasTag("bs")) {
const PacBio::BAM::Tag& tag = read.Impl().TagValue("bs");
std::vector<float> data = tag.ToFloatArray();
if (data.size() != 4) {
AddErrorMessage(
std::string("Tag BaseLineSigma must have 4 values per each record in read " +
read.FullName()));
}
float bls[4];
bls[baseMap_['A']] = data[0];
bls[baseMap_['C']] = data[1];
bls[baseMap_['G']] = data[2];
bls[baseMap_['T']] = data[3];
baseLineSigmaArray_.WriteRow(bls, 4);
} else {
AddErrorMessage(std::string("Tag BaseLineSigma is absent in read ") + read.FullName());
}
} else {
//BaseLineSigma won't be available uill v 3.0.1.
//AddErrorMessage("BaseLineSigma array is not initialized.");
}
return Errors().empty();
}
void HDFZMWWriter::Flush(void)
{
// Mandatory metrics
numEventArray_.Flush();
holeNumberArray_.Flush();
holeStatusArray_.Flush();
holeXYArray_.Flush();
// Optional metrics
if (HasBaseLineSigma()) baseLineSigmaArray_.Flush();
}
void HDFZMWWriter::Close(void)
{
this->Flush();
// Mandatory metrics
numEventArray_.Close();
holeNumberArray_.Close();
holeStatusArray_.Close();
holeXYArray_.Close();
// Optional metrics
if (HasBaseLineSigma()) baseLineSigmaArray_.Close();
zmwGroup_.Close();
}
bool HDFZMWWriter::InitializeChildHDFGroups(void)
{
// Mandatory metrics
if (numEventArray_.Initialize(zmwGroup_, PacBio::GroupNames::numevent) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::numevent);
}
if (holeNumberArray_.Initialize(zmwGroup_, PacBio::GroupNames::holenumber) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::holenumber);
}
if (holeStatusArray_.Initialize(zmwGroup_, PacBio::GroupNames::holestatus) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::holestatus);
}
if (holeXYArray_.Initialize(zmwGroup_, PacBio::GroupNames::holexy, 2) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::holexy);
}
/* BaseLineSigma not available until 3.0.1
if (InPulseCalls()) {
if (baseLineSigmaArray_.Initialize(zmwGroup_, PacBio::GroupNames::baselinesigma, 4) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(PacBio::GroupNames::baselinesigma);
}
}
*/
return Errors().empty();
}
void HDFZMWWriter::_WriteAttributes(void)
{
// NumEvent has no attributes.
if (holeNumberArray_.IsInitialized() and holeNumberArray_.size() > 0) {
AddAttribute<std::string>(holeNumberArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMW::HoleNumber::description);
}
if (holeStatusArray_.IsInitialized() and holeStatusArray_.size() > 0) {
AddAttribute<std::string>(holeStatusArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMW::HoleStatus::description);
/*
AddAttribute<std::vector<std::string>>(
holeStatusArray_, PacBio::AttributeNames::ZMW::HoleStatus::lookuptable,
PacBio::AttributeValues::ZMW::HoleStatus::lookuptable);
*/
}
if (holeXYArray_.IsInitialized() and holeXYArray_.GetNRows() > 0) {
AddAttribute<std::string>(holeXYArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMW::HoleXY::description);
}
if (HasBaseLineSigma() and baseLineSigmaArray_.GetNRows() > 0) {
AddAttribute<std::string>(baseLineSigmaArray_, PacBio::AttributeNames::Common::description,
PacBio::AttributeValues::ZMW::BaseLineSigma::description);
}
}
#endif
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