void HashErrorModel::setCell(const BaseData& data, char refBase)
{
if(ourUseFast)
{
if(mismatchTableFast.empty())
{
mismatchTableFast.resize(BaseData::getFastKeySize());
}
SMatchesFast& matchInfo = mismatchTableFast[data.getFastKey()];
if(BaseUtilities::areEqual(refBase, data.curBase))
{
++(matchInfo.m);
}
else
{
++(matchInfo.mm);
}
matchInfo.qempSimple = 255;
return;
}
SMatches& matchInfo = mismatchTable[data.getKey()];
if(BaseUtilities::areEqual(refBase, data.curBase))
{
++(matchInfo.m);
}
else
{
++(matchInfo.mm);
}
matchInfo.qempSimple = 255;
}
uint8_t HashErrorModel::getQemp(BaseData& data)
{
if(ourUseFast)
{
SMatchesFast& matchInfo = mismatchTableFast[data.getFastKey()];
// If no matches or mismatches, return the original quality.
if((matchInfo.m == 0) && (matchInfo.mm == 0))
{
return(data.qual);
}
if(matchInfo.qempSimple == 255)
{
matchInfo.qempSimple =
getQempSimple(matchInfo.m, matchInfo.mm);
}
return(matchInfo.qempSimple);
}
// If it is not in the table, return the original quality.
try
{
SMatches& matchMismatch = mismatchTable.at(data.getKey());
if(ourUseLogReg)
{
return(matchMismatch.qempLogReg);
}
if(matchMismatch.qempSimple == 255)
{
matchMismatch.qempSimple =
getQempSimple(matchMismatch.m, matchMismatch.mm);
}
return(matchMismatch.qempSimple);
}
catch(std::out_of_range& oor)
{
// just return the original quality.
return(data.qual);
}
}
