Skip to content

Commit

Permalink
multichrom cleanup for RemoveAllFixedMutations()
Browse files Browse the repository at this point in the history
  • Loading branch information
@bhaller
bhaller committed Nov 24, 2024
1 parent f3fd381 commit e580e0c
Show file tree
Hide file tree
Showing 2 changed files with 36 additions and 34 deletions.
6 changes: 5 additions & 1 deletion core/chromosome.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,11 @@ class Chromosome : public EidosDictionaryRetained
std::vector<double> hotspot_multipliers_M_;
std::vector<double> hotspot_multipliers_F_;

slim_usertag_t tag_value_ = SLIM_TAG_UNSET_VALUE; // a user-defined tag value
// private scratch space for the use of Population::RemoveAllFixedMutations()
std::vector<MutationIndex> fixed_mutation_accumulator_;

// a user-defined tag value
slim_usertag_t tag_value_ = SLIM_TAG_UNSET_VALUE;

Chromosome(const Chromosome&) = delete; // no copying
Chromosome& operator=(const Chromosome&) = delete; // no copying
Expand Down
64 changes: 31 additions & 33 deletions core/population.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8490,11 +8490,10 @@ void Population::RemoveAllFixedMutations(void)
if (child_generation_valid_)
EIDOS_TERMINATION << "ERROR (Population::RemoveAllFixedMutations): (internal error) called with child generation active!" << EidosTerminate();

// We use stack-local MutationRun objects so they get disposed of properly via RAII; non-optimal
// from a performance perspective, since they will do reallocs to reach their needed size, but
// We use a stack-local MutationRun object so it gets disposed of properly via RAII; non-optimal
// from a performance perspective, since it will do reallocs to reach its needed size, but
// since this method is only called once per cycle it shouldn't matter.
MutationRun removed_mutation_accumulator;
MutationRun fixed_mutation_accumulator;

#ifdef SLIMGUI
int mutation_type_count = static_cast<int>(species_.mutation_types_.size());
Expand Down Expand Up @@ -8587,8 +8586,8 @@ void Population::RemoveAllFixedMutations(void)
AddTallyForMutationTypeAndBinNumber(mutation_type_index, mutation_type_count, fixation_time / 10, &mutation_fixation_times_, &mutation_fixation_tick_slots_);
#endif

// add the fixed mutation to a vector, to be converted to a Substitution object below
fixed_mutation_accumulator.insert_sorted_mutation(mutation_index);
// add the fixed mutation to a per-chromosome vector, to be converted to a Substitution object below
chromosomes[mutation->chromosome_index_]->fixed_mutation_accumulator_.push_back(mutation_index);

mutation->state_ = MutationState::kFixedAndSubstituted; // marked in anticipation of removal below
remove_mutation = true;
Expand Down Expand Up @@ -8664,23 +8663,33 @@ void Population::RemoveAllFixedMutations(void)
}
#endif

// replace fixed mutations with Substitution objects
if (fixed_mutation_accumulator.size() > 0)
// replace fixed mutations with Substitution objects, one chromosome at a time
for (Chromosome *chromosome : chromosomes)
{
//std::cout << "Removing " << fixed_mutation_accumulator.size() << " fixed mutations..." << std::endl;
std::vector<MutationIndex> &fixed_mutation_accumulator = chromosome->fixed_mutation_accumulator_;
int fixed_mutation_accumulator_size = (int)fixed_mutation_accumulator.size();

if (fixed_mutation_accumulator_size == 0)
continue;

slim_chromosome_index_t chromosome_index = chromosome->Index();

//std::cout << "Chromosome " << chromosome_index << ": removing " << fixed_mutation_accumulator.size() << " fixed mutations..." << std::endl;

// We remove fixed mutations from each MutationRun just once; this is the operation ID we use for that
int haplosome_count_per_individual = species_.HaplosomeCountPerIndividual();
int first_haplosome_index = species_.FirstHaplosomeIndices()[chromosome_index];
int last_haplosome_index = species_.LastHaplosomeIndices()[chromosome_index];
int64_t operation_id = MutationRun::GetNextOperationID();

for (std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : subpops_) // subpopulations
{
Subpopulation *subpop = subpop_pair.second;

for (Individual *ind : subpop->parent_individuals_)
{
Haplosome **haplosomes = ind->haplosomes_;

for (int haplosome_index = 0; haplosome_index < haplosome_count_per_individual; haplosome_index++)
for (int haplosome_index = first_haplosome_index; haplosome_index <= last_haplosome_index; haplosome_index++)
{
Haplosome *haplosome = haplosomes[haplosome_index];

Expand All @@ -8690,27 +8699,16 @@ void Population::RemoveAllFixedMutations(void)
// for removal only within the runs that contain a mutation to be removed. If there is
// more than one mutation to be removed within the same run, the second time around the
// runs will no-op the scan using operation_id. The whole rest of the haplosomes can be skipped.
slim_chromosome_index_t haplosome_chr_index = haplosome->chromosome_index_;
slim_position_t mutrun_length = haplosome->mutrun_length_;

for (int mut_index = 0; mut_index < fixed_mutation_accumulator.size(); mut_index++)
for (int mut_index = 0; mut_index < fixed_mutation_accumulator_size; mut_index++)
{
MutationIndex mut_to_remove = fixed_mutation_accumulator[mut_index];
Mutation *mutation = (mut_block_ptr + mut_to_remove);

// We only try to remove a fixed mutation if it belongs to the haplosome's chromosome.
// Otherwise, it certainly isn't present, and the calculated mutrun_index might be out of range.
// FIXME MULTICHROM note that if there are many fixed mutations belonging to other chromosomes, we will
// waste a lot of time spinning here; would be better to organize the fixed mutations by chromosome,
// with a separate vector for each chromosome, and then handle each chromosome separately here...
if (mutation->chromosome_index_ == haplosome_chr_index)
{
slim_position_t mut_position = mutation->position_;
slim_mutrun_index_t mutrun_index = (slim_mutrun_index_t)(mut_position / mutrun_length);
slim_position_t mut_position = mutation->position_;
slim_mutrun_index_t mutrun_index = (slim_mutrun_index_t)(mut_position / mutrun_length);

// Note that total_haplosome_count_ is not needed by RemoveAllFixedMutations(); refcounts were set to -1 above.
haplosome->RemoveFixedMutations(operation_id, mutrun_index);
}
haplosome->RemoveFixedMutations(operation_id, mutrun_index);
}
}
}
Expand All @@ -8724,7 +8722,7 @@ void Population::RemoveAllFixedMutations(void)
{
// When doing tree recording, we additionally keep all fixed mutations (their ids) in a multimap indexed by their position
// This allows us to find all the fixed mutations at a given position quickly and easily, for calculating derived states
for (int i = 0; i < fixed_mutation_accumulator.size(); i++)
for (int i = 0; i < fixed_mutation_accumulator_size; i++)
{
Mutation *mut_to_remove = mut_block_ptr + fixed_mutation_accumulator[i];
Substitution *sub = new Substitution(*(mut_block_ptr + fixed_mutation_accumulator[i]), tick);
Expand All @@ -8736,26 +8734,26 @@ void Population::RemoveAllFixedMutations(void)
else
{
// When not doing tree recording, we just create substitutions and keep them in a vector
for (int i = 0; i < fixed_mutation_accumulator.size(); i++)
for (int i = 0; i < fixed_mutation_accumulator_size; i++)
substitutions_.emplace_back(new Substitution(*(mut_block_ptr + fixed_mutation_accumulator[i]), tick));
}

// Nucleotide-based models also need to modify the ancestral sequence when a mutation fixes
if (species_.IsNucleotideBased())
{
for (int i = 0; i < fixed_mutation_accumulator.size(); i++)
NucleotideArray *ancestral_seq = chromosome->ancestral_seq_buffer_;

for (int i = 0; i < fixed_mutation_accumulator_size; i++)
{
Mutation *mut_to_remove = mut_block_ptr + fixed_mutation_accumulator[i];

if (mut_to_remove->mutation_type_ptr_->nucleotide_based_)
{
Chromosome *mut_chromosome = species_.Chromosomes()[mut_to_remove->chromosome_index_];
NucleotideArray *ancestral_seq = mut_chromosome->ancestral_seq_buffer_;

ancestral_seq->SetNucleotideAtIndex(mut_to_remove->position_, mut_to_remove->nucleotide_);
}
}
}

// Clear the accumulator for reuse next tick
fixed_mutation_accumulator.clear();
}

// now we can delete (or zombify) removed mutation objects
Expand Down

0 comments on commit e580e0c

Please sign in to comment.