v4.3.7

CHANGELOG.md

@@ -1,6 +1,10 @@
 # Changelog
 The semantic versioning is kind of random.
 
+## 4.3.7
+### BugFix
+- When switching from exp. to Moran, do not try to add background mutations to cell if they have their last division time greater than `TIME_AT_BIRTH`. This is a problem when `tau-exp` is not correctly set.
+
 ## 4.3.6
 ### BugFix
 - The previous version didn't match the number of expanded clones from the SDE mode. So, we remove factor 2 and restore solution from `v4.3.4`, even though we initiate fit variants at size 2 instead of 1 (but has small prob. of p squared).

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "hsc"
-version = "4.3.6"
+version = "4.3.7"
 edition = "2021"
 
 [dependencies]

src/main.rs

@@ -136,6 +136,9 @@ fn main() {
                 proliferation,
                 options.gillespie_options.verbosity,
             );
+            if options.gillespie_options.verbosity > 0 {
+                println!("start simulating exp. phase");
+            }
 
             let stop = simulate(
                 state,
@@ -145,7 +148,7 @@ fn main() {
                 &options.gillespie_options,
                 rng,
             );
-            if options.gillespie_options.verbosity > 1 {
+            if options.gillespie_options.verbosity > 0 {
                 println!(
                     "exponential simulation {} stopped because {:#?}, nb cells {}",
                     idx,
@@ -165,6 +168,9 @@ fn main() {
             );
             let moran_distributions =
                 Distributions::new(probs_moran, app.options_moran.gillespie_options.verbosity);
+            if options.gillespie_options.verbosity > 0 {
+                println!("switching to moran");
+            }
             // switch_to_moran start with time 0
             exp.switch_to_moran(
                 ProcessOptions {
@@ -209,6 +215,9 @@ fn main() {
                 app.options_moran.gillespie_options.verbosity,
             )
         };
+        if app.options_moran.gillespie_options.verbosity > 0 {
+            println!("simulating Moran phase");
+        }
 
         let stop = simulate(
             state,

src/process.rs

@@ -123,13 +123,15 @@ impl Exponential {
                 println!("updating the neutral background mutations for all cells");
             }
             for stem_cell in self.subclones.get_mut_cells() {
-                assign_background_mutations(
-                    stem_cell,
-                    TIME_AT_BIRTH,
-                    &self.distributions.neutral_poisson,
-                    rng,
-                    self.verbosity,
-                );
+                if stem_cell.get_last_division_time() < &TIME_AT_BIRTH {
+                    assign_background_mutations(
+                        stem_cell,
+                        TIME_AT_BIRTH,
+                        &self.distributions.neutral_poisson,
+                        rng,
+                        self.verbosity,
+                    );
+                }
                 // this is required as we are restarting the time
                 stem_cell.set_last_division_time(0f32).unwrap();
             }