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ComputeAvgCoa_core.cpp
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ComputeAvgCoa_core.cpp
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/*
* ComputeAvgCoa_core
* Date: Jan-24-2013
* Author : Gabriel Renaud gabriel.reno [at sign here ] gmail.com
*
*/
#include "ComputeAvgCoa_core.h"
// #define DEBUG3
// damage (<-)
// transition (<->)
// A --------- G
// | |
// | |
// | |
// | |
// C --------- T
// transition (<->)
// damage ( ->)
inline bool isTransition(char allel_sample,char allel_reference,char allel_chimpHumanAncestor){
return (
(allel_sample == 'C' && (allel_reference == 'T' || (allel_chimpHumanAncestor == 'T') ) ) ||
(allel_sample == 'T' && (allel_reference == 'C' || (allel_chimpHumanAncestor == 'C') ) ) ||
(allel_sample == 'A' && (allel_reference == 'G' || (allel_chimpHumanAncestor == 'G') ) ) ||
(allel_sample == 'G' && (allel_reference == 'A' || (allel_chimpHumanAncestor == 'A') ) )
);
}
inline bool isDamage(char allel_sample,char allel_reference,char allel_chimpHumanAncestor){
return (
(allel_sample == 'T' && (allel_reference == 'C' || (allel_chimpHumanAncestor == 'C') ) ) ||
(allel_sample == 'A' && (allel_reference == 'G' || (allel_chimpHumanAncestor == 'G') ) )
);
}
void computeDiv(char allel_chimpHumanAncestor,char allel_reference,char allel_sample,bool isCpG,AvgCoaResult * divr){
if( (allel_chimpHumanAncestor == allel_reference ) && //no mutation
(allel_chimpHumanAncestor == allel_sample ) ){
//no need to call isTransition() isDamage() since no mutation
divr->all.counterSame++;
if(isCpG)
divr->onlyCpg.counterSame++;
else
divr->noCpg.counterSame++;
}
if( (allel_chimpHumanAncestor != allel_reference ) || //mutation occured
(allel_chimpHumanAncestor != allel_sample ) ){
if(allel_reference == allel_sample){ //common
#ifdef DEBUG3
cout<<"common"<<endl;
#endif
if(isTransition(allel_sample,allel_reference,allel_chimpHumanAncestor)){
divr->transitions.counterCommon++;
}else{
divr->transversions.counterCommon++;
}
if(!isDamage( allel_sample,allel_reference,allel_chimpHumanAncestor)){
divr->noDamage.counterCommon++;
}else{
}
divr->all.counterCommon++;
if(isCpG)
divr->onlyCpg.counterCommon++;
else
divr->noCpg.counterCommon++;
}
if( (allel_chimpHumanAncestor == allel_reference ) && //mutation occured in sample
(allel_chimpHumanAncestor != allel_sample ) ){
#ifdef DEBUG3
cout<<"sample"<<endl;
#endif
if(isTransition(allel_sample,allel_reference,allel_chimpHumanAncestor)){
divr->transitions.counterSample++;
}else{
divr->transversions.counterSample++;
}
if(!isDamage( allel_sample,allel_reference,allel_chimpHumanAncestor)){
divr->noDamage.counterSample++;
}
divr->all.counterSample++;
if(isCpG)
divr->onlyCpg.counterSample++;
else
divr->noCpg.counterSample++;
}
if( (allel_chimpHumanAncestor != allel_reference ) && //mutation occured in reference
(allel_chimpHumanAncestor == allel_sample ) ){
#ifdef DEBUG3
cout<<"reference"<<endl;
#endif
if(isTransition(allel_sample,allel_reference,allel_chimpHumanAncestor)){
divr->transitions.counterReference++;
}else{
divr->transversions.counterReference++;
}
if(!isDamage( allel_sample,allel_reference,allel_chimpHumanAncestor)){
divr->noDamage.counterReference++;
}
divr->all.counterReference++;
if(isCpG)
divr->onlyCpg.counterReference++;
else
divr->noCpg.counterReference++;
}
}
}