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#include <pbdata/reads/BaseFile.hpp>
#include <algorithm>
bool CompareHoleXY::operator()(const HoleXY &lhs, const HoleXY &rhs) const
{
if (lhs.xy[0] == rhs.xy[0]) {
return lhs.xy[1] < rhs.xy[1];
} else {
return lhs.xy[0] < rhs.xy[0];
}
}
bool BaseFile::LookupReadIndexByXY(uint16_t x, uint16_t y, UInt &index)
{
int16_t xy[2];
xy[0] = x;
xy[1] = y;
std::vector<HoleXY>::iterator holeIt;
holeIt = lower_bound(holeXY.begin(), holeXY.end(), xy);
if ((*holeIt).xy[0] == xy[0] and (*holeIt).xy[1] == xy[1]) {
index = holeIt - holeXY.begin();
return true;
} else {
return false;
}
}
void BaseFile::CopyReadAt(uint32_t readIndex, SMRTSequence &read)
{
assert(holeNumbers.size() > readIndex);
read.HoleNumber(holeNumbers[readIndex]);
if (holeXY.size() > 0) {
assert(holeXY.size() > readIndex);
read.HoleXY(holeXY[readIndex].xy[0], holeXY[readIndex].xy[1]);
}
DSLength startPos = readStartPositions[readIndex];
DNALength readLength = readLengths[readIndex];
read.length = readLength;
read.Allocate(readLength);
if (baseCalls.size() > 0) {
assert(baseCalls.size() >= readLength + startPos);
CopyArray(baseCalls, startPos, readLength, read.seq);
}
if (qualityValues.size() > 0) {
assert(qualityValues.size() >= readLength + startPos);
CopyArray(qualityValues, startPos, readLength, read.qual.data);
}
if (basWidthInFrames.size() > 0) {
assert(basWidthInFrames.size() >= readLength + startPos);
CopyArray(basWidthInFrames, startPos, readLength, read.widthInFrames);
}
if (deletionQV.size() > 0) {
assert(deletionQV.size() >= readLength + startPos);
CopyArray(deletionQV, startPos, readLength, read.deletionQV.data);
}
if (deletionTag.size() > 0) {
assert(deletionTag.size() >= readLength + startPos);
CopyArray(deletionTag, startPos, readLength, read.deletionTag);
}
if (insertionQV.size() > 0) {
assert(insertionQV.size() >= readLength + startPos);
CopyArray(insertionQV, startPos, readLength, read.insertionQV.data);
}
if (substitutionQV.size() > 0) {
assert(substitutionQV.size() >= readLength + startPos);
CopyArray(substitutionQV, startPos, readLength, read.substitutionQV.data);
}
if (mergeQV.size() > 0) {
assert(mergeQV.size() >= readLength + startPos);
CopyArray(mergeQV, startPos, readLength, read.mergeQV.data);
}
if (substitutionTag.size() > 0) {
assert(substitutionTag.size() >= readLength + startPos);
CopyArray(substitutionTag, startPos, readLength, read.substitutionTag);
}
if (preBaseFrames.size() > 0) {
assert(preBaseFrames.size() >= readLength + startPos);
CopyArray(preBaseFrames, startPos, readLength, read.preBaseFrames);
}
}
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