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bhallerbhaller
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multichrom changes for AssessMutationRuns() (debugging method)
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‎core/population.cpp‎

Lines changed: 63 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -6779,7 +6779,7 @@ void Population::UniqueMutationRuns(void)
67796779
std::clock_t end = std::clock();
67806780
double time_spent = static_cast<double>(end - begin) / CLOCKS_PER_SEC;
67816781

6782-
std::cout << "UniqueMutationRuns(): \n " << total_mutruns << " run pointers analyzed\n " << total_preexisting << " runs pre-existing\n " << total_uniqued_away << " duplicate runs discovered and uniqued away\n " << (total_mutruns - total_identical) << " final uniqued mutation runs\n " << total_hash_collisions << " hash collisions\n " << time_spent << " seconds elapsed" << std::endl;
6782+
std::cout << "UniqueMutationRuns(), tick " << community_.Tick() << ": \n " << total_mutruns << " run pointers analyzed\n " << total_preexisting << " runs pre-existing\n " << total_uniqued_away << " duplicate runs discovered and uniqued away\n " << (total_mutruns - total_identical) << " final uniqued mutation runs\n " << total_hash_collisions << " hash collisions\n " << time_spent << " seconds elapsed" << std::endl;
67836783
#else
67846784
// get rid of unused variable warnings
67856785
(void)total_hash_collisions;
@@ -7240,74 +7240,88 @@ void Population::AssessMutationRuns(void)
72407240

72417241
if (tick % 1000 == 0)
72427242
{
7243-
// First, unique our runs; this is just for debugging the uniquing, and should be removed. FIXME
7244-
int haplosome_count_per_individual = species_.HaplosomeCountPerIndividual();
7245-
slim_refcount_t total_haplosome_count = 0, total_mutrun_count = 0, total_shared_mutrun_count = 0;
7246-
int mutrun_count = 0, use_count_total = 0;
7247-
slim_position_t mutrun_length = 0;
7248-
int64_t mutation_total = 0;
7249-
7250-
int64_t operation_id = MutationRun::GetNextOperationID();
7243+
std::cout << "***** AssessMutationRuns(), tick " << tick << ":" << std::endl;
7244+
std::cout << " Mutation count: " << mutation_registry_.size() << std::endl;
72517245

7252-
for (const std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : subpops_)
7246+
for (Chromosome *chromosome : species_.Chromosomes())
72537247
{
7254-
Subpopulation *subpop = subpop_pair.second;
7248+
slim_chromosome_index_t chromosome_index = chromosome->Index();
7249+
int registry_size = 0, registry_count_in_chromosome = 0;
7250+
Mutation *mut_block_ptr = gSLiM_Mutation_Block;
7251+
const MutationIndex *registry = MutationRegistry(&registry_size);
72557252

7256-
for (Individual *ind : subpop->parent_individuals_)
7253+
for (int registry_index = 0; registry_index < registry_size; ++registry_index)
72577254
{
7258-
Haplosome **haplosomes = ind->haplosomes_;
7255+
Mutation *mut = mut_block_ptr + registry[registry_index];
72597256

7260-
for (int haplosome_index = 0; haplosome_index < haplosome_count_per_individual; haplosome_index++)
7257+
if (mut->chromosome_index_ == chromosome_index)
7258+
registry_count_in_chromosome++;
7259+
}
7260+
7261+
int first_haplosome_index = species_.FirstHaplosomeIndices()[chromosome_index];
7262+
int last_haplosome_index = species_.LastHaplosomeIndices()[chromosome_index];
7263+
int haplosome_count_per_individual = species_.HaplosomeCountPerIndividual();
7264+
slim_refcount_t total_haplosome_count = 0, total_mutrun_count = 0, total_shared_mutrun_count = 0;
7265+
int mutrun_count = 0, use_count_total = 0;
7266+
slim_position_t mutrun_length = 0;
7267+
int64_t mutation_total = 0;
7268+
7269+
int64_t operation_id = MutationRun::GetNextOperationID();
7270+
7271+
for (const std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : subpops_)
7272+
{
7273+
Subpopulation *subpop = subpop_pair.second;
7274+
7275+
for (Individual *ind : subpop->parent_individuals_)
72617276
{
7262-
Haplosome *haplosome = haplosomes[haplosome_index];
7277+
Haplosome **haplosomes = ind->haplosomes_;
72637278

7264-
if (!haplosome->IsNull())
7279+
for (int haplosome_index = first_haplosome_index; haplosome_index <= last_haplosome_index; haplosome_index++)
72657280
{
7266-
// FIXME MULTICHROM These values are different for different chromosomes,
7267-
// but get reported below as if they're all the same. This code doesn't
7268-
// really make much sense. Probably it needs to be restructured to report
7269-
// on one chromosome at a time.
7270-
mutrun_count = haplosome->mutrun_count_;
7271-
mutrun_length = haplosome->mutrun_length_;
7281+
Haplosome *haplosome = haplosomes[haplosome_index];
72727282

7273-
for (int run_index = 0; run_index < mutrun_count; ++run_index)
7283+
if (!haplosome->IsNull())
72747284
{
7275-
const MutationRun *mutrun = haplosome->mutruns_[run_index];
7276-
int mutrun_size = mutrun->size();
7277-
7278-
total_mutrun_count++;
7279-
mutation_total += mutrun_size;
7285+
mutrun_count = haplosome->mutrun_count_;
7286+
mutrun_length = haplosome->mutrun_length_;
72807287

7281-
if (mutrun->operation_id_ != operation_id)
7288+
for (int run_index = 0; run_index < mutrun_count; ++run_index)
72827289
{
7283-
slim_refcount_t use_count = (slim_refcount_t)mutrun->use_count();
7290+
const MutationRun *mutrun = haplosome->mutruns_[run_index];
7291+
int mutrun_size = mutrun->size();
72847292

7285-
total_shared_mutrun_count++;
7286-
use_count_total += use_count;
7293+
total_mutrun_count++;
7294+
mutation_total += mutrun_size;
72877295

7288-
mutrun->operation_id_ = operation_id;
7296+
if (mutrun->operation_id_ != operation_id)
7297+
{
7298+
slim_refcount_t use_count = (slim_refcount_t)mutrun->use_count();
7299+
7300+
total_shared_mutrun_count++;
7301+
use_count_total += use_count;
7302+
7303+
mutrun->operation_id_ = operation_id;
7304+
}
72897305
}
7306+
7307+
total_haplosome_count++;
72907308
}
7291-
7292-
total_haplosome_count++;
72937309
}
72947310
}
72957311
}
7312+
7313+
std::cout << " ========== Chromosome index " << (int)(chromosome->Index()) << ", id " << chromosome->ID() << ", symbol " << chromosome->Symbol() << " (length " << (chromosome->last_position_ + 1) << ")" << std::endl;
7314+
std::cout << " Mutation count in chromosome: " << registry_count_in_chromosome << std::endl;
7315+
std::cout << " Haplosome count: " << total_haplosome_count << " (divided into " << mutrun_count << " mutation runs of length " << mutrun_length << ")" << std::endl;
7316+
7317+
std::cout << " Mutation run unshared: " << total_mutrun_count;
7318+
if (total_mutrun_count) std::cout << " (containing " << (mutation_total / (double)total_mutrun_count) << " mutations on average)";
7319+
std::cout << std::endl;
7320+
7321+
std::cout << " Mutation run actual: " << total_shared_mutrun_count;
7322+
if (total_shared_mutrun_count) std::cout << " (mean use count " << (use_count_total / (double)total_shared_mutrun_count) << ")";
7323+
std::cout << std::endl;
72967324
}
7297-
7298-
std::cout << "***** Tick " << tick << ":" << std::endl;
7299-
std::cout << " Mutation count: " << mutation_registry_.size() << std::endl;
7300-
std::cout << " Haplosome count: " << total_haplosome_count << " (divided into " << mutrun_count << " mutation runs of length " << mutrun_length << ")" << std::endl;
7301-
7302-
std::cout << " Mutation run unshared: " << total_mutrun_count;
7303-
if (total_mutrun_count) std::cout << " (containing " << (mutation_total / (double)total_mutrun_count) << " mutations on average)";
7304-
std::cout << std::endl;
7305-
7306-
std::cout << " Mutation run actual: " << total_shared_mutrun_count;
7307-
if (total_shared_mutrun_count) std::cout << " (mean use count " << (use_count_total / (double)total_shared_mutrun_count) << ")";
7308-
std::cout << std::endl;
7309-
7310-
std::cout << "*****" << std::endl;
73117325
}
73127326
}
73137327

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