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_LpostPerCat
------------
1. produce it
gainLoss::startRate4Site
rate4siteGL::computeRate4site
computeEB_EXP_siteSpecificRate(_rates,_BayesianSTD,_BayesianLowerBound,_BayesianUpperBound,_sc,*_sp,_tr,_alphaConf,&_LpostPerCat,_unObservableData_p);
sperate:
LofPos_givenRateCat = likelihoodComputation::getLofPos(pos,et,sc,cpg[cat],sp);
pGivenR[cat] = LofPos_givenRateCat * sp.ratesProb(cat);
Assign:
if (LpostPerCat){
(*LpostPerCat)[j][pos]= convert(pGivenR[j]);
2. get it
_LpostPerCat = r4s.getLpostPerCat();
3. use it
startComputePosteriorExpectationOfChange(_sc,_tr,_sp,gainLossOptions::_outDir,_LpostPerCat);
if(LpostPerCat.size()==0 )
{
resizeMatrix(LpostPerCat,sp->categories(),sc.seqLen()) ;
if(sp->categories()>1){ // to fill LpostPerCat - run computeRate4site()
rate4siteGL r4s(sc,tr,sp,outDir, _unObservableData_p);
r4s.run();
LpostPerCat = r4s.getLpostPerCat();
}
else{
oneMatrix(LpostPerCat);
}
}
computeCountsGL countsGL(sc,tr,sp,outDir,LpostPerCat);
_expV01[pos]+=exp01*_LpostPerCat[rateIndex][pos];
_expV10[pos]+=exp10*_LpostPerCat[rateIndex][pos];
_probV01[pos]+=prob01*_LpostPerCat[rateIndex][pos];
_probV10[pos]+=prob10*_LpostPerCat[rateIndex][pos];
_probChanges_PosNodeXY[pos][i][j][k] += probChangesForBranchPerRateCategoryPerPos[i][j][k]*_LpostPerCat[rateIndex][pos];
_expChanges_PosNodeXY[pos][i][j][k] += expChangesForBranchPerRateCategoryPerPos[i][j][k]*_LpostPerCat[rateIndex][pos];
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