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#include "Bias.h"
#include <smithwaterman/convert.h>
void Bias::open(string& file) {
ifstream input;
input.open(file.c_str());
if (!input.is_open()) {
cerr << "allele reference bias description " << file << " is not open" << endl;
exit(1);
}
string line;
bool firstrecord = true;
int last;
while (std::getline(input, line)) {
vector<string> fields = split(line, " \t");
if (firstrecord) {
convert(fields[0], minLength);
last = minLength - 1;
}
convert(fields[0], maxLength);
if (maxLength != last + 1) {
cerr << "gap or out-of-order bias list in " << file << endl;
cerr << line << endl;
exit(1);
} else {
last = maxLength;
}
long double dbias;
convert(fields[1], dbias);
biases.push_back(dbias);
}
input.close();
}
long double Bias::bias(int length) {
if (biases.empty()) return 1; // no bias
if (length < minLength) {
return biases.front();
} else if (length > maxLength) {
return biases.back();
} else {
return biases.at(length - minLength);
}
}
bool Bias::empty(void) {
return biases.empty();
}
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