/usr/include/pbihdf/HDFPlsReader.hpp is in libpbihdf-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
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#define _BLASR_HDF_PLS_READER_HPP_
#include "HDFArray.hpp"
#include "HDF2DArray.hpp"
#include "HDFAtom.hpp"
#include "HDFGroup.hpp"
#include "HDFBasReader.hpp"
#include "HDFPulseDataFile.hpp"
#include "DatasetCollection.hpp"
#include "HDFZMWReader.hpp"
#include "reads/PulseFile.hpp"
#include "HDFScanDataReader.hpp"
#include "FASTQSequence.hpp"
#include "VectorUtils.hpp"
#include <sstream>
#include <vector>
#include <set>
using namespace H5;
using namespace std;
/*
* Interface for reading pulse information from a .pls.h5 file.
* To read both pls and bas information, use the HDFBasReader.
*/
class HDFPlsReader : public DatasetCollection, public HDFPulseDataFile {
DNALength curPos;
int curRead;
HDFGroup pulseCallsGroup;
int meanSignalNDims, midSignalNDims, maxSignalNDims;
HDF2DArray<uint16_t> meanSignalMatrix;
HDF2DArray<uint16_t> midSignalMatrix;
HDF2DArray<uint16_t> maxSignalMatrix;
HDFArray<uint16_t> meanSignalArray;
HDFArray<uint16_t> midSignalArray;
HDFArray<uint16_t> maxSignalArray;
HDFArray<uint16_t> plsWidthInFramesArray;
HDFArray<unsigned int> startFrameArray;
HDFArray<float> classifierQVArray;
public:
HDFPlsReader() : HDFPulseDataFile(), DatasetCollection() {
fieldNames.push_back("MeanSignal");
fieldNames.push_back("MidSignal");
fieldNames.push_back("MaxSignal");
fieldNames.push_back("StartFrame");
fieldNames.push_back("ClassifierQV");
fieldNames.push_back("WidthInFrames");
fieldNames.push_back("FrameRate");
fieldNames.push_back("WhenStarted");
fieldNames.push_back("NumEvent"); // this is read from the zmw, but control it here.
InitializeAllFields(false);
}
int InitializeCommon() {
return 1;
}
int Initialize(string hdfPlsFileName, const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT) {
/*
* Initialize access to the HDF file.
*/
if (HDFPulseDataFile::Initialize(hdfPlsFileName, fileAccPropList) == 0) {
return 0;
}
if (pulseDataGroup.ContainsObject("PulseCalls") == 0 or
pulseCallsGroup.Initialize(pulseDataGroup.group, "PulseCalls") == 0) {
return 0;
}
zmwReader.Initialize(&pulseCallsGroup);
//
// Initialize arrays for reading. This has been preconfigured to
//
if (!InitializePulseGroup()) return 0;
if ( (meanSignalNDims = GetDatasetNDim(pulseCallsGroup.group, "MeanSignal")) == 1) {
if (!meanSignalArray.Initialize(pulseCallsGroup, "MeanSignal")) return 0;
}
else if (meanSignalNDims == 2) {
if (!meanSignalMatrix.Initialize(pulseCallsGroup, "MeanSignal")) return 0;
}
if ((midSignalNDims = GetDatasetNDim(pulseCallsGroup.group, "MidSignal")) == 1) {
if (!midSignalArray.Initialize(pulseCallsGroup, "MidSignal")) return 0;
}
else if (midSignalNDims == 2) {
if (!midSignalMatrix.Initialize(pulseCallsGroup, "MidSignal")) return 0;
}
if ((maxSignalNDims = GetDatasetNDim(pulseCallsGroup.group, "MaxSignal")) == 1) {
if (!maxSignalArray.Initialize(pulseCallsGroup, "MaxSignal")) return 0;
}
else if (maxSignalNDims == 2) {
if (!maxSignalMatrix.Initialize(pulseCallsGroup, "MaxSignal")) return 0;
}
//
// Astro pulse files may not have the ClassifierQV dataset, check
// to see if it exists, and then try and initialize it.
//
if (pulseCallsGroup.ContainsObject("ClassifierQV")) {
if (!classifierQVArray.Initialize(pulseCallsGroup, "ClassifierQV")) return 0;
} else {
includedFields["ClassifierQV"] = false;
}
//
// These are all required fields.
//
if (!startFrameArray.Initialize(pulseCallsGroup, "StartFrame")) return 0;
if (!plsWidthInFramesArray.Initialize(pulseCallsGroup, "WidthInFrames")) return 0;
curRead = 0;
nReads = zmwReader.numEventArray.arrayLength;
return 1;
}
UInt GetStartFrameSize() {
return startFrameArray.arrayLength;
}
void GetAllMeanSignal(vector<uint16_t> &meanSignal) {
if (meanSignalNDims == 1) {
CheckMemoryAllocation(meanSignalArray.arrayLength, maxAllocNElements, "MeanSignal");
meanSignal.resize(meanSignalArray.arrayLength);
meanSignalArray.Read(0, meanSignalArray.arrayLength, &meanSignal[0]);
}
else if (meanSignalNDims == 2) {
CheckMemoryAllocation(meanSignalMatrix.GetNCols() * meanSignalMatrix.GetNRows(), maxAllocNElements, "MeanSignal");
meanSignal.resize(meanSignalMatrix.GetNCols() * meanSignalMatrix.GetNRows());
meanSignalMatrix.Read(0, meanSignalMatrix.GetNRows(), &meanSignal[0]);
}
}
void GetAllMidSignal(vector<uint16_t> &midSignal) {
if (midSignalNDims == 1) {
CheckMemoryAllocation(midSignalArray.arrayLength, maxAllocNElements, "MidSignal");
midSignal.resize(midSignalArray.arrayLength);
midSignalArray.Read(0, midSignalArray.arrayLength, &midSignal[0]);
}
else if (midSignalNDims == 2) {
CheckMemoryAllocation(midSignalMatrix.GetNCols() * midSignalMatrix.GetNRows(), maxAllocNElements, "MidSignal");
midSignal.resize(midSignalMatrix.GetNCols() * midSignalMatrix.GetNRows());
midSignalMatrix.Read(0, midSignalMatrix.GetNRows(), &midSignal[0]);
}
}
void GetAllMaxSignal(vector<uint16_t> &maxSignal) {
if (maxSignalNDims == 1) {
CheckMemoryAllocation(maxSignalArray.arrayLength, maxAllocNElements, "MaxSignal");
maxSignal.resize(maxSignalArray.arrayLength);
maxSignalArray.Read(0, maxSignalArray.arrayLength, &maxSignal[0]);
}
else if (maxSignalNDims == 2) {
CheckMemoryAllocation(maxSignalMatrix.GetNCols() * maxSignalMatrix.GetNRows(), maxAllocNElements, "MaxSignal");
maxSignal.resize(maxSignalMatrix.GetNCols() * maxSignalMatrix.GetNRows());
maxSignalMatrix.Read(0, maxSignalMatrix.GetNRows(), &maxSignal[0]);
}
}
void GetAllStartFrames(vector<UInt> &startFrame) {
CheckMemoryAllocation(startFrameArray.arrayLength, maxAllocNElements, "StartFrame");
startFrame.resize(startFrameArray.arrayLength);
startFrameArray.Read(0,startFrameArray.arrayLength, &startFrame[0]);
}
void GetAllPlsWidthInFrames(vector<uint16_t> &widthInFrames) {
CheckMemoryAllocation(plsWidthInFramesArray.arrayLength, maxAllocNElements, "WidthInFrames (pulse)");
widthInFrames.resize(plsWidthInFramesArray.arrayLength);
plsWidthInFramesArray.Read(0,plsWidthInFramesArray.arrayLength, &widthInFrames[0]);
}
void GetAllClassifierQV(vector<float> &classifierQV) {
CheckMemoryAllocation(classifierQVArray.arrayLength, maxAllocNElements, "ClassifierQV (pulse)");
classifierQV.resize(classifierQVArray.arrayLength);
classifierQVArray.Read(0, classifierQVArray.arrayLength, &classifierQV[0]);
}
void GetAllNumEvent(vector<int> &numEvent) {
CheckMemoryAllocation(zmwReader.numEventArray.arrayLength, maxAllocNElements, "NumEvent (pulse)");
numEvent.resize(zmwReader.numEventArray.arrayLength);
zmwReader.numEventArray.Read(0, zmwReader.numEventArray.arrayLength, &numEvent[0]);
}
// Always call ReadPulseFileInit before calling ReadPulseFile()
// or ReadField()
void ReadPulseFileInit(PulseFile & pulseFile) {
if (scanDataReader.fileHasScanData) {
scanDataReader.Read(pulseFile.scanData);
}
// Get hole numbers in PulseCalls/ZMW/HoleNumber. Note that
// PulseCalls/ZMW/HoleNumber and BaseCalls/ZMW/HoleNumber are
// not always identical.
GetAllHoleNumbers(pulseFile.holeNumbers);
// By default, always get the num event. This is used
// later to copy reads from the pls file.
GetAllNumEvent(pulseFile.numEvent);
assert(pulseFile.holeNumbers.size() == pulseFile.numEvent.size());
if (pulseFile.numEvent.size() > 0) {
pulseFile.pulseStartPositions.resize(pulseFile.numEvent.size());
pulseFile.pulseStartPositions[0] = 0;
for (int i = 1; i < pulseFile.numEvent.size(); i++) {
pulseFile.pulseStartPositions[i] = pulseFile.pulseStartPositions[i-1] +
pulseFile.numEvent[i-1];
}
}
}
void ReadPulseFile(PulseFile &pulseFile) {
ReadPulseFileInit(pulseFile);
if (includedFields["StartFrame"]) {
GetAllStartFrames(pulseFile.startFrame);
}
if (includedFields["WidthInFrames"]) {
GetAllPlsWidthInFrames(pulseFile.plsWidthInFrames);
}
if (includedFields["MeanSignal"]) {
GetAllMeanSignal(pulseFile.meanSignal);
pulseFile.meanSignalNDims = meanSignalNDims;
}
if (includedFields["MidSignal"]) {
GetAllMidSignal(pulseFile.midSignal);
pulseFile.midSignalNDims = midSignalNDims;
}
if (includedFields["MaxSignal"]) {
GetAllMaxSignal(pulseFile.maxSignal);
pulseFile.maxSignalNDims = maxSignalNDims;
}
if (includedFields["ClassifierQV"]) {
GetAllClassifierQV(pulseFile.classifierQV);
}
}
//
// Return size of the entire field in KB.
//
UInt GetFieldSize(const string & field) {
if (not includedFields[field]) {
cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
exit(1);
}
if (field == "StartFrame") {
return startFrameArray.arrayLength / 1024 * sizeof(unsigned int);
} else if (field == "WidthInFrames") {
return plsWidthInFramesArray.arrayLength / 1024 * sizeof (uint16_t);
} else if (field == "MeanSignal") {
return meanSignalArray.arrayLength / 1024 * sizeof(uint16_t);
} else if (field == "MidSignal") {
return midSignalArray.arrayLength / 1024 * sizeof(uint16_t);
} else if (field == "MaxSignal") {
return maxSignalArray.arrayLength / 1024 * sizeof(uint16_t);
} else if (field == "NumEvent") {
return zmwReader.numEventArray.arrayLength / 1024 * sizeof (int);
} else if (field == "ClassifierQV") {
return classifierQVArray.arrayLength /1024 * sizeof(float);
} else {
cout << "ERROR, field [" << field << "] is not supported. " << endl ;
exit(1);
}
}
//
// Read the entire field to memory
//
void ReadField(PulseFile & pulseFile, const string & field) {
if (not includedFields[field]) {
cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
exit(1);
}
if (field == "StartFrame") {
GetAllStartFrames(pulseFile.startFrame);
} else if (field == "WidthInFrames") {
GetAllPlsWidthInFrames(pulseFile.plsWidthInFrames);
} else if (field == "MeanSignal") {
GetAllMeanSignal(pulseFile.meanSignal);
pulseFile.meanSignalNDims = meanSignalNDims;
} else if (field == "MidSignal") {
GetAllMidSignal(pulseFile.midSignal);
pulseFile.midSignalNDims = midSignalNDims;
} else if (field == "MaxSignal") {
GetAllMaxSignal(pulseFile.maxSignal);
pulseFile.maxSignalNDims = maxSignalNDims;
} else if (field == "NumEvent") {
GetAllNumEvent(pulseFile.numEvent);
} else if (field == "ClassifierQV") {
// GetAllClassifierQV(pulseFile.classifierQV) is equivalent to
// classifierQVArray.ReadDataset(pulseFile.classifierQV) with
// memory check
GetAllClassifierQV(pulseFile.classifierQV);
} else {
cout << "ERROR, field [" << field << "] is not supported. " << endl ;
exit(1);
}
}
// Copy a field for a hole
void CopyFieldAt(PulseFile & pulseFile, const string & field,
int holeIndex, int * basToPlsIndex,
void * dest, int destLength, const string & destSequence="") {
Nucleotide * destSeqCopy = NULL;
if (destSequence != "") {
destSeqCopy = ProtectedNew<Nucleotide>(destSequence.size());
for(int i = 0 ; i < destSequence.size(); i++) {
destSeqCopy[i] = (Nucleotide)destSequence[i];
}
}
if (not includedFields[field]) {
cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
exit(1);
}
UInt pulseStartPos= pulseFile.pulseStartPositions[holeIndex];
if (field == "StartFrame") {
assert(pulseFile.startFrame.size() > 0 and
pulseFile.startFrame.size() > pulseStartPos);
StoreField(pulseFile.startFrame, basToPlsIndex, ((UInt*)dest), destLength);
} else if (field == "WidthInFrames") {
assert(pulseFile.plsWidthInFrames.size() > 0 and
pulseFile.plsWidthInFrames.size() > pulseStartPos);
StoreField(pulseFile.plsWidthInFrames, basToPlsIndex, (uint16_t*)dest, destLength);
} else if (field == "MeanSignal") {
assert(pulseFile.meanSignal.size() > 0 and
pulseFile.meanSignal.size() > pulseStartPos);
assert(destLength == destSequence.size());
pulseFile.CopySignal((HalfWord*)(&pulseFile.meanSignal[0]),
meanSignalNDims,
0, //basToPlsIndex maps bases to abs pulse positions
basToPlsIndex,
destSeqCopy, destLength,
(HalfWord*)dest);
} else if (field == "MidSignal") {
assert(pulseFile.midSignal.size() > 0 and
pulseFile.midSignal.size() > pulseStartPos);
assert(destLength == destSequence.size());
pulseFile.CopySignal((HalfWord*)(&pulseFile.midSignal[0]),
midSignalNDims,
0, //basToPlsIndex maps bases to abs pulse positions
basToPlsIndex,
destSeqCopy, destLength,
(HalfWord*)dest);
} else if (field == "MaxSignal") {
assert(pulseFile.maxSignal.size() > 0 and
pulseFile.maxSignal.size() > pulseStartPos);
assert(destLength == destSequence.size());
pulseFile.CopySignal((HalfWord*)(&pulseFile.maxSignal[0]),
maxSignalNDims,
0, //basToPlsIndex maps bases to abs pulse positions
basToPlsIndex,
destSeqCopy, destLength,
(HalfWord*)dest);
} else if (field == "ClassifierQV") {
assert(pulseFile.classifierQV.size() > 0 and
pulseFile.classifierQV.size() > pulseStartPos);
StoreField(pulseFile.classifierQV, basToPlsIndex, (float*)dest, destLength);
} else if (field == "NumEvent") {
cout << "ERROR, control of copying numEvent should not go here." << endl;
exit(1);
} else {
cout << "ERROR, field [" << field << "] is not supported. " << endl ;
exit(1);
}
if (destSeqCopy != NULL) {
delete [] destSeqCopy;
}
}
// Clear memory allocated for the specified field
void ClearField(PulseFile & pulseFile, const string & field) {
if (not includedFields[field]) {
cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
exit(1);
}
if (field == "StartFrame") {
ClearMemory(pulseFile.startFrame);
} else if (field == "WidthInFrames") {
ClearMemory(pulseFile.plsWidthInFrames);
} else if (field == "MeanSignal") {
ClearMemory(pulseFile.meanSignal);
pulseFile.meanSignalNDims = -1;
} else if (field == "MidSignal") {
ClearMemory(pulseFile.midSignal);
pulseFile.midSignalNDims = -1;
} else if (field == "MaxSignal") {
ClearMemory(pulseFile.maxSignal);
pulseFile.maxSignalNDims = -1;
} else if (field == "NumEvent") {
ClearMemory(pulseFile.numEvent);
} else if (field == "ClassifierQV") {
ClearMemory(pulseFile.classifierQV);
} else {
cout << "ERROR, field [" << field << "] is not supported. " << endl ;
exit(1);
}
}
int GetReadAt(int holeNumber, int* &basToPlsIndex, SMRTSequence &read) {
if (preparedForRandomAccess == false) {
PrepareForRandomAccess();
}
curRead = holeNumber;
curPos = eventOffset[holeNumber];
zmwReader.curZMW = holeNumber;
return GetNextFlattenedToBase(read, basToPlsIndex);
}
template<typename T_FieldType>
void StoreField(vector<T_FieldType> &source, int *basToPlsIndex, T_FieldType *dest, int destLength) {
int i;
for (i = 0 ; i < destLength; i++) {
dest[i] = source[basToPlsIndex[i]];
}
}
void ReadSignal(string fieldName,
HDFArray<HalfWord> &signalArray, HDF2DArray<HalfWord> &signalMatrix,
int plsSeqLength, int nDims,
Nucleotide *basSeq, int basSeqLength,
int *basToPlsIndex, HalfWord* dest) {
if (includedFields[fieldName]) {
vector<HalfWord> signal;
if (nDims == 2) {
signal.resize(plsSeqLength * 4);
signalMatrix.Read(curPos, curPos + plsSeqLength, &signal[0]); // read off one row.
int i;
for (i = 0; i < basSeqLength; i++) {
dest[i] = signal[basToPlsIndex[i]*4 + scanDataReader.BaseMap()[basSeq[i]]];
}
}
else {
signal.resize(plsSeqLength);
signalArray.Read(curPos, curPos + plsSeqLength, &signal[0]);
int i;
for (i = 0; i < basSeqLength; i++) {
dest[i] = signal[basToPlsIndex[i]];
}
}
}
}
int GetNextFlattenedToBase(SMRTSequence &read, int* basToPlsIndex) {
/*
* Get the pulse values, but only store values that correspond to called bases.
* This requires that the read has the read.seq field assigned.
*/
assert(read.seq != NULL);
int seqLength;
try{
//
// Find out how many pulses are called for this read.
zmwReader.numEventArray.Read(curRead, curRead+1, &seqLength);
if (includedFields["StartFrame"]) {
vector<unsigned int> pulseStartFrame;
pulseStartFrame.resize(seqLength);
startFrameArray.Read(curPos, curPos + seqLength, &pulseStartFrame[0]);
if (read.startFrame) {delete [] read.startFrame; read.startFrame = NULL;}
read.startFrame = ProtectedNew<unsigned int>(read.length);
StoreField(pulseStartFrame, basToPlsIndex, read.startFrame, read.length);
}
if (includedFields["WidthInFrames"]) {
vector<HalfWord> pulseWidthInFrames;
pulseWidthInFrames.resize(seqLength);
plsWidthInFramesArray.Read(curPos, curPos + seqLength, &pulseWidthInFrames[0]);
if (read.widthInFrames) {delete [] read.widthInFrames; read.widthInFrames = NULL;}
read.widthInFrames = ProtectedNew<HalfWord>(read.length);
StoreField(pulseWidthInFrames, basToPlsIndex, read.widthInFrames, read.length);
}
if (includedFields["MidSignal"]) {
if (read.midSignal) {delete [] read.midSignal; read.midSignal = NULL;}
read.midSignal = ProtectedNew<HalfWord>(read.length);
ReadSignal("MidSignal", midSignalArray, midSignalMatrix, seqLength, midSignalNDims,
read.seq, read.length, basToPlsIndex, read.midSignal);
}
if (includedFields["MaxSignal"]) {
if (read.maxSignal) {delete [] read.maxSignal; read.maxSignal = NULL;}
read.maxSignal = ProtectedNew<HalfWord>(read.length);
ReadSignal("MaxSignal", maxSignalArray, maxSignalMatrix, seqLength, maxSignalNDims,
read.seq, read.length, basToPlsIndex, read.maxSignal);
}
if (includedFields["MeanSignal"]) {
if (read.meanSignal) {delete [] read.meanSignal; read.meanSignal = NULL;}
read.meanSignal = ProtectedNew<HalfWord>(read.length);
ReadSignal("MeanSignal", meanSignalArray, meanSignalMatrix, seqLength, meanSignalNDims,
read.seq, read.length, basToPlsIndex, read.meanSignal);
}
if (includedFields["ClassifierQV"]) {
vector<float> pulseClassifierQV;
pulseClassifierQV.resize(seqLength);
classifierQVArray.Read(curPos, curPos + seqLength, &pulseClassifierQV[0]);
if (read.classifierQV) {delete [] read.classifierQV; read.classifierQV = NULL;}
read.classifierQV = ProtectedNew<float>(read.length);
StoreField(pulseClassifierQV, basToPlsIndex, read.classifierQV, read.length);
}
curRead++;
curPos += seqLength;
} catch (DataSetIException e) {
cout << "ERROR, could not read pulse metrics for SMRTSequence "
<< read.GetName() << endl;
exit(1);
}
return 1;
}
void Close() {
}
};
#endif
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