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// Author: Mark Chaisson
#include "PulseFile.hpp"
void PulseFile::CopySignal(HalfWord *signalData, // either a vector or matrix
int signalNDims,
DSLength pulseStartPos, // 0 if baseToPulseIndex maps to abs position
int *baseToPulseIndex,
Nucleotide *readSeq,
DNALength readLength,
HalfWord *readData) {
// if baseToPulseIndex maps bases to absolute pulse postions
// pulseStartPos must be 0;
// otherwise, pulseStartPos is pulseStartPositions[holeIndex]
std::map<char, size_t> baseMap = GetBaseMap();
if (signalNDims == 1) {
for (DNALength i = 0; i < readLength; i++) {
readData[i] = signalData[pulseStartPos + baseToPulseIndex[i] ];
}
}
else {
for (DNALength i = 0; i < readLength; i++) {
readData[i] = signalData[baseToPulseIndex[i]*4 + baseMap[readSeq[i]]];
}
}
}
void PulseFile::CopyReadAt(uint32_t plsReadIndex, int *baseToPulseIndex, SMRTSequence &read) {
DSLength pulseStartPos = pulseStartPositions[plsReadIndex];
bool OK = true;
if (midSignal.size() > 0) {
assert(midSignal.size() > pulseStartPos);
OK = Realloc(read.midSignal, read.length);
CopySignal(&midSignal[0],
midSignalNDims,
pulseStartPos,
baseToPulseIndex,
read.seq, read.length,
read.midSignal);
}
if (maxSignal.size() > 0) {
assert(maxSignal.size() > pulseStartPos);
OK = OK and Realloc(read.maxSignal, read.length);
CopySignal(&maxSignal[0],
maxSignalNDims,
pulseStartPos,
baseToPulseIndex,
read.seq, read.length,
read.maxSignal);
}
if (meanSignal.size() > 0) {
assert(meanSignal.size() > pulseStartPos);
OK = OK and Realloc(read.meanSignal, read.length);
CopySignal(&meanSignal[0],
meanSignalNDims,
pulseStartPos,
baseToPulseIndex,
read.seq, read.length,
read.meanSignal);
}
if (plsWidthInFrames.size() > 0) {
OK = OK and Realloc(read.widthInFrames, read.length);
StoreField(plsWidthInFrames, baseToPulseIndex, read.widthInFrames, read.length);
}
if (classifierQV.size() > 0) {
OK = OK and Realloc(read.classifierQV, read.length);
StoreField(classifierQV, baseToPulseIndex, read.classifierQV, read.length);
}
if (startFrame.size() > 0) {
OK = OK and Realloc(read.startFrame, read.length);
StoreField(startFrame, baseToPulseIndex, read.startFrame, read.length);
}
if (not OK) {
std::cout << "ERROR, failed to CopyReadAt(" << plsReadIndex << ")" << std::endl;
exit(1);
}
}
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