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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/>.
*/
/*
* ObservationModel.hpp
*
* Created on: Apr 2, 2009
* Author: caa
*/
#ifndef OBSERVATIONMODEL_HPP_
#define OBSERVATIONMODEL_HPP_
#include <iostream>
#include <string>
using namespace std;
class ObservationModelParameters
{
public:
ObservationModelParameters() {
modelType="probabilistic";
setDefaultValues();
}
ObservationModelParameters(const string & modelType) {
if (modelType=="threshold" || modelType=="probabilistic") this->modelType=modelType; else throw string("Model not supported.");
setDefaultValues();
}
void setDefaultValues()
{
pError=1e-4;
baseQualThreshold=0.995;
fixedBaseQual=0.99;
maxLengthIndel=10;
mapQualThreshold=100.0;
capMapQualFast=40.0;
scaleErr=0.95;
numE=3;
pMut=1e-4;
minOverlap=0;
numIndels=1;
indelDist="exponential";
maxLengthDel=maxLengthIndel;
pFirstgLO=0.01;
checkBaseQualThreshold = 0.95;
bMid=-1;
forceReadOnHaplotype=false;
mapUnmappedReads = false;
padCover=5;
maxMismatch=1;
maxTryHash=5;
}
void print()
{
cout << "\tmodelType: " << modelType << endl;
cout << "\tmaxLengthIndel: " << maxLengthIndel << " pError: " << pError << endl;
cout << "\tbaseQualThreshold: " << baseQualThreshold << " fixedBaseQual: " << fixedBaseQual << endl;
cout << "\tmapQualThreshold: " << mapQualThreshold << endl;
cout << "\tcapMapQualFast: " << capMapQualFast << endl;
cout << "\tminOverlap: " << minOverlap << endl;
cout << "\tscaleError: " << scaleErr << endl;
cout << "\tnumE: " << numE << endl;
cout << "\tpMut: " << pMut << endl;
cout << "\tnumIndels: " << numIndels << endl;
cout << "\tindelDistribution: " << indelDist << endl;
cout << "\tmaxLengthDel: " << maxLengthDel << " pError: " << pError << endl;
cout << "\tpFirstgLO: " << pFirstgLO << endl;
cout << "\tpadCover: " << padCover << endl;
cout << "\tmaxMismatch: " << maxMismatch << endl;
cout << "\tmaxTryHash: " << maxTryHash << endl;
cout << "\tcheckBaseQualThreshold: " << checkBaseQualThreshold << endl;
cout << "\tmapUnmappedReads: " << mapUnmappedReads << endl;
//cout << "\tlogLikThreshod: " << logLikThreshold << endl;
}
double pError, baseQualThreshold, fixedBaseQual, mapQualThreshold, capMapQualFast, scaleErr, pMut;
int maxLengthIndel, numE, minOverlap, numIndels, bMid;
double checkBaseQualThreshold;
string modelType, indelDist;
int maxLengthDel,maxTryHash;
bool forceReadOnHaplotype, mapUnmappedReads;
double pFirstgLO;
int padCover, maxMismatch;
};
#endif /* OBSERVATIONMODEL_HPP_ */
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