F3_core.cpp

/*
 * F3_core
 * Date: Mar-15-2013 
 * Author : Gabriel Renaud gabriel.reno [at sign here ] gmail.com
 *
 */

#include "F3_core.h"
#include "ComputeAvgCoa_core.h"




bool addCountersInd(const int  refCount,
		    const int  altCount,
		    const bool isCpG,
		    const bool isSitePotentialTransition, 
		    const bool isSitePotentialDamage,
		    F3Result * f3res){
    //cerr<<"addCountersInd "<<refCount<<" "<<altCount<<endl;
    f3res->all.addAlleleCounts(refCount,altCount);
    if(isCpG){
	f3res->onlyCpg.addAlleleCounts(refCount,altCount);
    }else{
	f3res->noCpg.addAlleleCounts(refCount,altCount);
    }

    if(  isSitePotentialTransition ){
	f3res->transitions.addAlleleCounts(refCount,altCount);
    }else{
	f3res->transversions.addAlleleCounts(refCount,altCount);
    }
    if( !isSitePotentialDamage ){
	f3res->noDamage.addAlleleCounts(refCount,altCount);
    }//TODO check!
        
}

bool computeF3triple(const double freq_condition,//target
		     const double freq_ind1,
		     const double freq_ind2,
		     const bool isCpG,//true if CpG
		     const bool isSitePotentialTransition, //true if transition
		     const bool isSitePotentialDamage, //true if damage
		     F3Result * f3res){

    
    double f3=(freq_condition-freq_ind1)*(freq_condition-freq_ind2);
    //cerr<<f3<<"\t"<<freq_condition<<"\t"<<freq_ind1<<"\t"<<freq_condition<<"\t"<<freq_ind2<<"\t"<<f3res->all.f3Sum<<endl;

    f3res->all.f3Sum                 += f3;
    //cerr<<f3<<"\t"<<freq_condition<<"\t"<<freq_ind1<<"\t"<<freq_condition<<"\t"<<freq_ind2<<"\t"<<f3res->all.f3Sum<<endl;
    //cerr<<"counterSites1 "<<f3res->all.counterSites<<endl;
    f3res->all.counterSites ++;
    //cerr<<"counterSites2 "<<f3res->all.counterSites<<endl;
    if(isCpG){
	f3res->onlyCpg.f3Sum         += f3;
	f3res->onlyCpg.counterSites  ++;

    }else{
	f3res->noCpg.f3Sum           += f3;
	f3res->noCpg.counterSites++;
    }

    if(  isSitePotentialTransition ){
	f3res->transitions.f3Sum     += f3;
	f3res->transitions.counterSites++;

    }else{
	f3res->transversions.f3Sum   += f3;
	f3res->transversions.counterSites++;
    }
    if( !isSitePotentialDamage ){
	f3res->noDamage.f3Sum        += f3;
	f3res->noDamage.counterSites++;
    }//TODO check!


    return false;
        
}