Skip to content

fix: symmetric N/* handling across strands in PWM energy routines (5.11.11) #150

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
aviezerl merged 1 commit into from
Jul 21, 2026
Merged

fix: symmetric N/* handling across strands in PWM energy routines (5.11.11) #150

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: misha
Title: Toolkit for Analysis of Genomic Data
Version: 5.11.10
Version: 5.11.11
Authors@R: c(
person("Misha", "Hoichman", , "misha@hoichman.com", role = "aut"),
person("Aviezer", "Lifshitz", , "aviezer.lifshitz@weizmann.ac.il", role = c("aut", "cre")),
Expand Down
4 changes: 4 additions & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
# misha 5.11.11

* **Internal consistency:** `N`/`*` are now scored the same on both strands in the PWM energy routines (reverse used `log(0.25)`, forward used the column average; both now use the average). No behavior change for genomic scoring, where `N`-windows are masked to `-Inf`; keeps `DnaPSSM` in sync with the `prego` package.

# misha 5.11.10

* **Behavior fix:** non-multitask `gintervals.quantiles()` (`options(gmultitasking = FALSE)`) no longer truncates the result to the first ~1000 intervals on a large scope; the streaming (`intervals.set.out=`) and in-memory results now match the multitasking output (#149).
Expand Down
6 changes: 3 additions & 3 deletions src/DnaPSSM.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -915,7 +915,7 @@ void DnaPSSM::integrate_energy(const string &target, float &energy, vector<float
break;
}
if(DnaLookupTables::NEUTRAL_CHAR[(unsigned char)*j]) {
logp += c_log_quarter;
logp += p->get_avg_log_prob();
} else {
int code = DnaLookupTables::COMPLEMENT_ENCODE[(unsigned char)*j];
if(code >= 0) {
Expand Down Expand Up @@ -986,7 +986,7 @@ void DnaPSSM::integrate_energy_logspat(const string &target, float &energy, vect
break;
}
if(DnaLookupTables::NEUTRAL_CHAR[(unsigned char)*j]) {
logp += c_log_quarter;
logp += p->get_avg_log_prob();
} else {
int code = DnaLookupTables::COMPLEMENT_ENCODE[(unsigned char)*j];
if(code >= 0) {
Expand Down Expand Up @@ -1058,7 +1058,7 @@ void DnaPSSM::integrate_energy_max_logspat(const string &target, float &energy,
break;
}
if(DnaLookupTables::NEUTRAL_CHAR[(unsigned char)*j]) {
logp_rev += c_log_quarter;
logp_rev += p->get_avg_log_prob();
} else {
int code = DnaLookupTables::COMPLEMENT_ENCODE[(unsigned char)*j];
if(code >= 0) {
Expand Down