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#include <pbdata/PrettyException.hpp>
#include <pbdata/alignment/CmpAlignment.hpp>
std::map<std::string, int> CmpAlignmentBase::columnNameToIndex;
unsigned int *CmpAlignmentBase::GetAlignmentIndex() { return &alignmentIndex[0]; }
int CmpAlignmentBase::GetAlignmentIndexSize() { return alignmentIndex.size(); }
unsigned int CmpAlignmentBase::GetAlignedStrand() { return LookupColumnValue("AlignedStrand"); }
unsigned int CmpAlignmentBase::GetRCRefStrand() { return LookupColumnValue("RCRefStrand"); }
// synonym
unsigned int CmpAlignmentBase::GetTStrand() { return GetRCRefStrand(); }
bool CmpAlignmentBase::GetX(int &xp)
{
if (alignmentIndex.size() > 0) {
xp = alignmentIndex[columnNameToIndex["x"]];
return true;
} else {
xp = -1;
return false;
}
}
unsigned int CmpAlignmentBase::GetAlignmentId() { return LookupColumnValue("AlnID"); }
unsigned int CmpAlignmentBase::GetX() { return LookupColumnValue("x"); }
unsigned int CmpAlignmentBase::GetY() { return LookupColumnValue("y"); }
unsigned int CmpAlignmentBase::GetMovieId() { return LookupColumnValue("MovieId"); }
unsigned int CmpAlignmentBase::GetAlnGroupId() { return LookupColumnValue("AlnGroupId"); }
unsigned int CmpAlignmentBase::GetReadGroupId() { return LookupColumnValue("ReadGroupId"); }
unsigned int CmpAlignmentBase::LookupColumnValue(const char *columnName)
{
if (columnNameToIndex.find(columnName) != columnNameToIndex.end()) {
int columnIndex = columnNameToIndex[columnName];
return alignmentIndex[columnIndex];
} else {
std::cout << "ERROR, For now cmp files must contain a column " << columnName << std::endl;
std::cout << "size of columnNameToIndex: " << columnNameToIndex.size() << std::endl;
BLASR_THROW(columnName + std::string{" does not contain a column!"});
}
}
void CmpAlignmentBase::InitializeColumnNameToIndex(std::vector<std::string> &columnNames)
{
for (size_t i = 0; i < columnNames.size(); i++) {
columnNameToIndex[columnNames[i]] = i;
}
}
unsigned int CmpAlignmentBase::GetHoleNumber() { return LookupColumnValue("HoleNumber"); }
unsigned int CmpAlignmentBase::GetRefGroupId() { return LookupColumnValue("RefGroupId"); }
unsigned int CmpAlignmentBase::GetRefSeqId() { return LookupColumnValue("RefSeqId"); }
unsigned int CmpAlignmentBase::GetOffsetBegin() { return LookupColumnValue("offset_begin"); }
unsigned int CmpAlignmentBase::GetOffsetEnd() { return LookupColumnValue("offset_end"); }
unsigned int CmpAlignmentBase::GetQueryStart() { return LookupColumnValue("rStart"); }
unsigned int CmpAlignmentBase::GetQueryEnd() { return LookupColumnValue("rEnd"); }
unsigned int CmpAlignmentBase::GetRefStart() { return LookupColumnValue("tStart"); }
unsigned int CmpAlignmentBase::GetRefEnd() { return LookupColumnValue("tEnd"); }
unsigned int CmpAlignmentBase::GetNMatch() { return LookupColumnValue("nM"); }
unsigned int CmpAlignmentBase::GetNMismatch() { return LookupColumnValue("nMM"); }
unsigned int CmpAlignmentBase::GetNInsertions() { return LookupColumnValue("nIns"); }
unsigned int CmpAlignmentBase::GetNDeletions() { return LookupColumnValue("nDel"); }
unsigned int CmpAlignmentBase::GetMapQV() { return LookupColumnValue("MapQV"); }
unsigned int CmpAlignmentBase::GetSubreadId() { return LookupColumnValue("SubreadId"); }
unsigned int CmpAlignmentBase::GetStrobeNumber() { return LookupColumnValue("StrobeNumber"); }
unsigned int CmpAlignmentBase::GetSetNumber() { return LookupColumnValue("SetNumber"); }
CmpAlignmentBase::CmpAlignmentBase(PlatformId platformIdP) { platformId = platformIdP; }
void CmpAlignmentBase::SetPlatformId(PlatformId platformIdP) { platformId = platformIdP; }
// CmpAlignment
CmpAlignment::CmpAlignment(PlatformId pid) : CmpAlignmentBase(pid) {}
void CmpAlignment::StoreAlignmentIndex(unsigned int *alignmentIndexPtr,
DSLength alignmentIndexLength)
{
alignmentIndex.clear();
alignmentIndex.insert(alignmentIndex.begin(), &alignmentIndexPtr[0],
&alignmentIndexPtr[alignmentIndexLength]);
}
void CmpAlignment::StoreAlignmentArray(unsigned char *alignmentArrayPtr,
DSLength alignmentArrayLength)
{
alignmentArray.resize(alignmentArrayLength);
for (DSLength a = 0; a < alignmentArrayLength; a++) {
alignmentArray[a] = alignmentArrayPtr[a];
}
}
CmpAlignment &CmpAlignment::operator=(const CmpAlignment &rhs)
{
// deep copy the alignment index
alignmentIndex.resize(rhs.alignmentIndex.size());
copy(rhs.alignmentIndex.begin(), rhs.alignmentIndex.end(), alignmentIndex.begin());
// deep copy the alignment array
alignmentArray.resize(rhs.alignmentIndex.size());
copy(rhs.alignmentArray.begin(), rhs.alignmentArray.end(), alignmentArray.begin());
// copy fields
Z = rhs.Z;
index = rhs.index;
readGroupId = rhs.readGroupId;
movieId = rhs.movieId;
refSeqId = rhs.refSeqId;
expId = rhs.expId;
runId = rhs.runId;
panel = rhs.panel;
x = rhs.x;
y = rhs.y;
rcRefStrand = rhs.rcRefStrand;
holeNumber = rhs.holeNumber;
offsetBegin = rhs.offsetBegin;
offsetEnd = rhs.offsetEnd;
setNumber = rhs.setNumber, strobeNumber = rhs.strobeNumber, mapQV = rhs.mapQV,
nBackRead = rhs.nBackRead, nReadOverlap = rhs.nReadOverlap;
subreadId = rhs.subreadId;
nMatch = rhs.nMatch, nMismatch = rhs.nMismatch, nIns = rhs.nIns, nDel = rhs.nDel;
return *this;
}
int CmpAlignment::operator<(const CmpAlignment &rhs) const
{
if (alignmentArray[1] == rhs.alignmentArray[1]) {
if (alignmentArray[2] == rhs.alignmentArray[2]) {
if (alignmentArray[10] == rhs.alignmentArray[10]) {
return (alignmentArray[4] < rhs.alignmentArray[4]);
} else {
return alignmentArray[10] < rhs.alignmentArray[10];
}
} else {
return alignmentArray[2] < rhs.alignmentArray[2];
}
} else {
return alignmentArray[1] < rhs.alignmentArray[1];
}
}
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