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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "Chooser.h"
#include <code/Mock/common_functions.h>
void Chooser::chooseWithPairedReads(ExtensionData*m_ed,
double __PAIRED_MULTIPLIER,
vector<set<int> >*battleVictories,
Parameters*parameters
){
vector<int> minimumValues;
vector<int> counts;
vector<int> maximumValues;
for(int i=0;i<(int)m_ed->m_enumerateChoices_outgoingEdges.size();i++){
int minimum=999999;
int maximum=-999;
Kmer key=m_ed->m_enumerateChoices_outgoingEdges[i];
for(int j=0;j<(int)m_ed->m_EXTENSION_pairedReadPositionsForVertices[key].size();j++){
int value=m_ed->m_EXTENSION_pairedReadPositionsForVertices[key][j];
if(value>maximum){
maximum=value;
}
if(value<minimum){
minimum=value;
}
}
counts.push_back(m_ed->m_EXTENSION_pairedReadPositionsForVertices[key].size());
if(m_ed->m_EXTENSION_pairedReadPositionsForVertices[key].size()==0){
minimum=0;
maximum=0;
}
minimumValues.push_back(minimum);
maximumValues.push_back(maximum);
}
for(int i=0;i<(int)m_ed->m_enumerateChoices_outgoingEdges.size();i++){
if(counts[i]==0){
continue;
}
for(int j=0;j<(int)m_ed->m_enumerateChoices_outgoingEdges.size();j++){
if(maximumValues[i] > __PAIRED_MULTIPLIER*maximumValues[j]){
(*battleVictories)[i].insert(j);
}
// same maximum
if(maximumValues[i] <= __PAIRED_MULTIPLIER*maximumValues[j]
&& maximumValues[j] <= __PAIRED_MULTIPLIER*maximumValues[i]
&& counts[i]>20*counts[j]){
// dodge sequencing errors.
(*battleVictories)[i].insert(j);
}
}
}
}
void Chooser::clear(int*a,int b){
while(b!=0){
a[--b]=0;
}
}
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