void loop()
{
rows.push_back(new Column);
rows.back()->label.assign("CHROM");
rows.push_back(new Column);
rows.back()->label.assign("POS");
rows.push_back(new Column);
rows.back()->label.assign("ID");
rows.push_back(new Column);
rows.back()->label.assign("REF");
rows.push_back(new Column);
rows.back()->label.assign("ALT");
for(int i=0;i< samples.size();++i)
{
Sample* sample=samples.at(i);
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":QUAL");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":FILTER");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":INFO");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":FORMAT");
rows.push_back(new Column);
rows.back()->label.assign(sample->name).append(":CALL");
}
screen=Screen::startup();
screen->border();
screen->refresh();
for(;;)
{
int c=screen->getch();
switch(c)
{
case 'q':
{
break;
}
case
}
}
Screen::shutdown();
}
void run(std::istream& in)
{
vector<string> tokens;
string line;
int chromCol=0;
int posCol=1;
int idCol=2;
int refCol=3;
int altCol=4;
int sampleCol=-1;
while(getline(in,line,'\n'))
{
if(AbstractApplication::stopping()) break;
if(line.empty() || line[0]=='#') continue;
tokenizer.split(line,tokens);
string chrom=tokens[chromCol];
chat *p2;
int pos=(int)strtol(tokens[posCol].c_str(),&p2,10);
string id=tokens[idCol];
string ref=tokens[refCol];
string alt=tokens[altCol];
string sampleName=tokens[sampleCol];
Row* therow=NULL;
if(!rows.empty() &&
rows.back()->pos->chrom.compare(chrom)==0 &&
rows.back()->pos->pos==pos &&
rows.back()->ref.compare(ref)==0 &&
rows.back()->alt.compare(alt)==0
)
{
therow=rows.back();
}
else
{
therow=new Row;
therow->pos=new ChromPosition(chrom,pos);
therow->id.assign(id);
therow->ref.assign(ref);
therow->alt.assign(alt);
rows.push_back(therow);
}
int index_sample=0;
if(sampleCol==-1)
{
if(sample2col.empty())
{
Sample* sample=new Sample;
sample->name.assign("Sample");
sample->column_index=0;
samples.push_back(sample);
}
index_sample=0;
}
else
{
map<string,Sample*>::iterator r= sample2col.find(sampleName);
if(r==sample2col.end())
{
Sample* sample=new Sample;
sample->name.assign(sampleName);
sample->column_index=sample2col.size();
index_sample=sample->column_index;
samples.push_back(sample);
sample2col.put(sample->name,sample);
}
else
{
index_sample=r->second->column_index;
}
}
if(index_sample>=therow->data.size())
{
therow->data.resize(index_sample+1);
}
Data* data=new Data;
therow->data.assign(index_sample,data);
}
}
