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Fix -wslr/-wslm .sitelh invariant under per-category (safe_numeric) scaling #534

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Fix -wslr/-wslm .sitelh invariant under per-category (safe_numeric) scaling #534

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10 changes: 8 additions & 2 deletions tree/phylotree.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1539,7 +1539,10 @@ void PhyloTree::computePatternLikelihood(double *ptn_lh, double *cur_logl, doubl
double *lh_cat = _pattern_lh_cat;
double *out_lh_cat = ptn_lh_cat;
UBYTE *nei2_scale = nei2->scale_num;
if (params->lk_safe_scaling || leafNum >= params->numseq_safe_scaling) {
// NOTE: must match the kernel's per-category vs per-pattern scaling choice
// (PhyloTree::safe_numeric, set in setLikelihoodKernel), otherwise scale_num
// is mis-indexed and the per-category log-likelihoods are off by a scale step.
if (safe_numeric) {
// per-category scaling
for (ptn = 0; ptn < nptn; ptn++) {
for (i = 0; i < ncat; i++) {
Expand All @@ -1565,7 +1568,10 @@ void PhyloTree::computePatternLikelihood(double *ptn_lh, double *cur_logl, doubl
double *out_lh_cat = ptn_lh_cat;
UBYTE *nei1_scale = nei1->scale_num;
UBYTE *nei2_scale = nei2->scale_num;
if (params->lk_safe_scaling || leafNum >= params->numseq_safe_scaling) {
// NOTE: must match the kernel's per-category vs per-pattern scaling choice
// (PhyloTree::safe_numeric, set in setLikelihoodKernel), otherwise scale_num
// is mis-indexed and the per-category log-likelihoods are off by a scale step.
if (safe_numeric) {
// per-category scaling
for (ptn = 0; ptn < nptn; ptn++) {
for (i = 0; i < ncat; i++) {
Expand Down