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#include "Contamination.h"
#include <smithwaterman/convert.h>
void Contamination::open(string& file) {
ifstream input;
input.open(file.c_str());
if (!input.is_open()) {
cerr << "contamination estimates file " << file << " is not open" << endl;
exit(1);
}
string line;
int last;
while (std::getline(input, line)) {
vector<string> fields = split(line, " \t");
if (fields.size() != 3) {
cerr << "could not parse contamination estimate:" << endl
<< line << endl
<< "should be of the form:" << endl
<< "sample p(read=R|genotype=AR) p(read=A|genotype=AA)" << endl;
exit(1);
}
string sample = fields[0];
ContaminationEstimate c;
convert(fields[1], c.probRefGivenHet);
convert(fields[2], c.probRefGivenHomAlt);
if (sample == "*") { // default
defaultEstimate = c;
} else {
insert(make_pair(sample, c));
}
}
input.close();
}
double Contamination::probRefGivenHet(string& sample) {
Contamination::iterator s = find(sample);
if (s != end()) {
return s->second.probRefGivenHet;
} else {
return defaultEstimate.probRefGivenHet;
}
}
double Contamination::probRefGivenHomAlt(string& sample) {
Contamination::iterator s = find(sample);
if (s != end()) {
return s->second.probRefGivenHomAlt;
} else {
return defaultEstimate.probRefGivenHomAlt;
}
}
double Contamination::refBias(string& sample) {
Contamination::iterator s = find(sample);
if (s != end()) {
return s->second.refBias;
} else {
return defaultEstimate.refBias;
}
}
ContaminationEstimate& Contamination::of(string& sample) {
Contamination::iterator s = find(sample);
if (s != end()) {
return s->second;
} else {
return defaultEstimate;
}
}
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