// extract from each line different columns
// and give them to further processing
int processLine(stringList columns, int qualThreshold, int covThreshold, int &seqCount)
{
string transcriptID, pos, refbase, reads, baseQuals;
int cov;
if (columns.size() == 6)
{
cov = atoi(columns[3].c_str());
refbase = columns[2];
if (cov > covThreshold)
{
transcriptID = columns[0];
pos = columns[1];
reads = columns[4];
baseQuals = columns[5];
assert (baseQuals.length() == cov) ;
extractMismatches(reads,baseQuals,cov, transcriptID,pos,refbase, qualThreshold, seqCount);
}
}
return 0;
}
//Get all Name in order
bool PWM::_getOrderedPositionNames(stringList& pos, stringList& names){
for(size_t i=0;i<pos.size();i++){
size_t nameHeader=pos[i].find("NAME:");
if (nameHeader == std::string::npos){
continue;
}
size_t nameLineEnding=pos[i].find_first_of("\n",nameHeader);
std::string name = pos[i].substr(nameHeader+5,nameLineEnding-(nameHeader+5));
clear_whitespace(name, " \t\n");
if (names.contains(name)){
std::cerr << "Position with name of: " << name << " is defined twice in the model\n";
return false;
}
else{
names.push_back(name);
}
}
return true;
}
// extract from each line different columns
// and give them to further processing
void processLine( stringList columns, int qualThreshold, int coverageThreshold)
{
if (columns[2] != "N" && columns[2] != "." && columns[2] != "_" )
{
string transcriptID, pos, ref, reads, baseQuals;
int cov;
if (columns.size() == 6)
{
cov = atoi(columns[3].c_str());
if (cov > coverageThreshold)
{
transcriptID = columns[0];
pos = columns[1];
ref = columns[2];
reads = columns[4];
baseQuals = columns[5];
assert ( baseQuals.length() == cov ) ;
extractMismatches(reads, baseQuals, cov, transcriptID,
pos, ref, qualThreshold, coverageThreshold);
}
}
}
}
//define extra field
int findField(stringList columns,string &XGfield,
string &NMfield, string &MDfield)
{
int i;
string field;
for (i = 10 ; i < columns.size(); i++)
{
field = columns[i];
if (field.substr(0,2) == "XG")
{
XGfield = field;
}
else if (field.substr(0,2) == "NM")
{
NMfield = field;
}
else if (field.substr(0,2) == "MD")
{
MDfield = field;
}
}
return 0;
}