fix #642, unreferenced mutation from multiple reload

Author: bhaller

VERSIONS

@@ -185,7 +185,8 @@ multitrait branch:
 		(float$)calcVA(object<Individual> individuals, [Nio<MutationType>$ mutType = NULL], [Niso<Trait>$ trait = NULL]): additive genetic variance
 		(float$)calcVD(object<Individual> individuals, [Nio<MutationType>$ mutType = NULL], [Niso<Trait>$ trait = NULL]): dominance genetic variance
 		(float$)calcVG(object<Individual> individuals, [Nio<MutationType>$ mutType = NULL], [Niso<Trait>$ trait = NULL]): total genetic variance
-	fix #641, a crash related to expanding the mutation block buffers when reading in from a file (whether .trees, VCF, MS, or SLiM format), or inside addNew[Drawn]Mutation()
+	fix #641, a crash related to expanding the mutation block buffers when reading in from a file (whether .trees, VCF, MS, or SLiM format), or inside addNew[Drawn]Mutation() (new in multitrait)
+	fix #642, mutations retained by the tree not re-retained by the tree when a saved tree sequence file is reloaded (new in multitrait)
 
 
 version 5.2 (Eidos version 4.2):

core/species.cpp

@@ -12897,11 +12897,6 @@ void Species::__CreateMutationsFromTabulation(std::unordered_map<slim_mutationid
 		if (gSLiM_next_mutation_id <= mutation_id)
 			gSLiM_next_mutation_id = mutation_id + 1;
 
-		// a mutation might not be referenced by any extant haplosome; it might be present in an ancestral node,
-		// but have been lost in all descendants, in which case we do not need to instantiate it
-		if (mut_info.ref_count == 0)
-			continue;
-		
 #if DEBUG
 		// BCH 2/13/2026: We used to do a memcpy() here to give us an aligned copy of metadata_ptr, but in the
 		// new metadata design the pointer should always be to an aligned address; we error here if not
@@ -12943,14 +12938,34 @@ void Species::__CreateMutationsFromTabulation(std::unordered_map<slim_mutationid
 
 			Mutation *new_mut = new (mut_block_ptr + new_mut_index) Mutation(mutation_id, mutation_type_ptr, chromosome_index, position, metadata_ptr);
 
-			// add it to our local map, so we can find it when making haplosomes, and to the population's mutation registry
-			p_mutIndexMap[mutation_id] = new_mut_index;
-			population_.MutationRegistryAdd(new_mut, /* p_autogenerated */ false);
-			
+			// a mutation might not be referenced by any extant haplosome; it might be present in an ancestral node,
+			// but have been lost in all descendants, in which case we do not need to instantiate it
+			// BCH 7/16/2026: Now we DO instantiate such mutations; they are "retained by the tree",
+			// since they are referenced by an ancestral derived state somewhere in the tree sequence
+			if (mut_info.ref_count == 0)
+			{
+				// it is legal to read a .trees file in without tree-seq mutations enabled; in that case,
+				// there is no such thing as "retained by the tree" so we can just ignore these mutations
+				if (RecordingTreeSequenceMutations())
+				{
+					muts_retained_by_treeseq_.push_back(new_mut_index);
+					any_muts_retained_impermanently_ = true;			// we don't know here, so we assume true
+					
+					//new_mut->Retain();	// new mutations already have a retain count of 1; we take that over here, as MutationRegistryAdd() does
+					new_mut->retained_by_treeseq_ = true;
+				}
+			}
+			else
+			{
+				// add it to our local map, so we can find it when making haplosomes, and to the population's mutation registry
+				p_mutIndexMap[mutation_id] = new_mut_index;
+				population_.MutationRegistryAdd(new_mut, /* p_autogenerated */ false);
+				
 #ifdef SLIM_KEEP_MUTTYPE_REGISTRIES
-			if (population_.keeping_muttype_registries_)
-				EIDOS_TERMINATION << "ERROR (Species::__CreateMutationsFromTabulation): (internal error) separate muttype registries set up during pop load." << EidosTerminate();
+				if (population_.keeping_muttype_registries_)
+					EIDOS_TERMINATION << "ERROR (Species::__CreateMutationsFromTabulation): (internal error) separate muttype registries set up during pop load." << EidosTerminate();
 #endif
+			}
 		}
 	}
 }