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Don't check for duplicate haplosome IDs #554

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Merged
bhaller merged 1 commit into from
Sep 7, 2025
Merged

Don't check for duplicate haplosome IDs #554

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31 changes: 12 additions & 19 deletions core/species.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8727,6 +8727,7 @@ void Species::__CreateSubpopulationsFromTabulation(std::unordered_map<slim_objec
// This could be done with a hash table, but I imagine that would be slower until the number of individuals becomes very large
// Also, I'm a bit nervous about putting a large number of consecutive integers into a hash table, re: edge-case performance
std::vector<slim_pedigreeid_t> pedigree_id_check;
std::vector<slim_haplosomeid_t> haplosome_id_check;

gSLiM_next_pedigree_id = 0;

Expand Down Expand Up @@ -8806,12 +8807,16 @@ void Species::__CreateSubpopulationsFromTabulation(std::unordered_map<slim_objec
individual->spatial_z_ = subpop_info.spatial_z_[tabulation_index];

p_nodeToHaplosomeMap.emplace(node_id_0, individual->haplosomes_[first_haplosome_index]);
individual->haplosomes_[first_haplosome_index]->haplosome_id_ = pedigree_id * 2;
slim_haplosomeid_t haplosome_id = pedigree_id * 2;
individual->haplosomes_[first_haplosome_index]->haplosome_id_ = haplosome_id;
haplosome_id_check.emplace_back(haplosome_id); // we will test for collisions below

if (last_haplosome_index != first_haplosome_index)
{
p_nodeToHaplosomeMap.emplace(node_id_1, individual->haplosomes_[last_haplosome_index]);
individual->haplosomes_[last_haplosome_index]->haplosome_id_ = pedigree_id * 2 + 1;
haplosome_id = pedigree_id * 2 + 1;
individual->haplosomes_[last_haplosome_index]->haplosome_id_ = haplosome_id;
haplosome_id_check.emplace_back(haplosome_id); // we will test for collisions below
}

// check the referenced nodes; right now this is not essential for re-creating the saved state, but is just a crosscheck
Expand Down Expand Up @@ -9814,13 +9819,12 @@ void Species::__CheckNodePedigreeIDs(__attribute__((unused)) EidosInterpreter *p
// could be nodes in the node table with haplosome pedigree IDs greater than those in use by individuals, in nonWF models.
// See https://github.com/MesserLab/SLiM/pull/420 for an example model that does this very easily.

// Also, check for duplicate pedigree IDs, just in case. __CreateSubpopulationsFromTabulation() does this for individual
// pedigree IDs; we do it for node pedigree IDs. I decided to use a vector with std::sort() to check even though it is
// O(n log n), rather than a hash table for O(n), because I'm nervous about hitting a bad edge case with the hash table
// due to the nature of the values being inserted. Shouldn't be a big deal in the grand scheme of things.
// Previously, we checked for duplicate haplosome IDs here as well, just in case.
// __CreateSubpopulationsFromTabulation() does this in living individuals
// already; however, it was found to be overly restrictive, in situations
// involving merging of parallel simulations; see https://github.com/MesserLab/SLiM/issues/538
tsk_node_table_t &node_table = tables.nodes;
tsk_size_t node_count = node_table.num_rows;
std::vector<slim_haplosomeid_t> haplosome_id_check;

for (tsk_size_t j = 0; (size_t)j < node_count; j++)
{
Expand All @@ -9833,11 +9837,7 @@ void Species::__CheckNodePedigreeIDs(__attribute__((unused)) EidosInterpreter *p
{
// get the metadata record and check the haplosome pedigree ID
HaplosomeMetadataRec *metadata_rec = (HaplosomeMetadataRec *)(node_table.metadata + offset1);
slim_haplosomeid_t haplosome_id = metadata_rec->haplosome_id_;

haplosome_id_check.emplace_back(haplosome_id); // we will test for collisions below

slim_pedigreeid_t pedigree_id = haplosome_id / 2; // rounds down to integer
slim_pedigreeid_t pedigree_id = metadata_rec->haplosome_id_ / 2; // rounds down to integer

if (pedigree_id >= gSLiM_next_pedigree_id)
{
Expand All @@ -9854,13 +9854,6 @@ void Species::__CheckNodePedigreeIDs(__attribute__((unused)) EidosInterpreter *p
}
}
}

// Check for haplosome pedigree ID collisions by sorting and looking for duplicates
std::sort(haplosome_id_check.begin(), haplosome_id_check.end());
const auto duplicate = std::adjacent_find(haplosome_id_check.begin(), haplosome_id_check.end());

if (duplicate != haplosome_id_check.end())
EIDOS_TERMINATION << "ERROR (Species::__CheckNodePedigreeIDs): the haplosome pedigree ID value " << *duplicate << " was used more than once; haplosome pedigree IDs must be unique." << EidosTerminate();
}

void Species::_ReadAncestralSequence(const char *p_file, Chromosome &p_chromosome)
Expand Down
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