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/*
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* ReadIndelErrorModel.hpp
*
* Created on: Oct 12, 2009
* Author: caa
*/
#ifndef READINDELERRORMODEL_HPP_
#define READINDELERRORMODEL_HPP_
class ReadIndelErrorModel
{
public:
ReadIndelErrorModel()
{
double hp[] = { 2.9e-5, 2.9e-5,2.9e-5, 2.9e-5, 4.3e-5, 1.1e-4, 2.4e-4, 5.7e-4, 1.0e-3, 1.4e-3 };
baselineProbs = vector<double>(10,0.0);
for (int x=0;x<10;x++) {
baselineProbs[x]=hp[x];
}
}
double getViterbiHPError(int hpLen)
{
int len=hpLen;
if (len<1) len=1;
double pbe;
if (len<=10) {
pbe=baselineProbs[len-1];
} else {
pbe=baselineProbs[9]+4.3e-4*double(len-10);
}
pbe *= double(hpLen);
if (pbe>0.99) pbe = 0.99;
return pbe;
}
private:
vector<double> baselineProbs;
};
#endif /* READINDELERRORMODEL_HPP_ */
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