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simpler maybe? #667

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113 changes: 28 additions & 85 deletions core/species.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8790,51 +8790,19 @@ void Species::DerivedStatesFromMetadata(tsk_table_collection_t *p_tables)
assert(mutation_table.metadata != nullptr);
assert(mutation_table.metadata_offset != nullptr);

// Swap the derived state column and the metadata column; after this, binary derived states will be in the
// derived state column and ASCII derived states will be in the metadata column.
std::swap(mutation_table.derived_state_length, mutation_table.metadata_length);
std::swap(mutation_table.max_derived_state_length, mutation_table.max_metadata_length);
std::swap(mutation_table.max_derived_state_length_increment, mutation_table.max_metadata_length_increment);
std::swap(mutation_table.derived_state, mutation_table.metadata);
std::swap(mutation_table.derived_state_offset, mutation_table.metadata_offset);

// Then empty out the metadata column, which we don't use while simulating; we want to free up the buffer
// for the metadata, rather than having the (perhaps large capacity) buffer hanging around forever. The
// best way to do this without using (much) private information is to (a) init a new mutation table,
// (b) use tsk_mutation_table_takeset_columns() to set up that table with our number of rows but with
// empty metadata (setting up whatever internal representation our version of tskit prefers for that),
// (c) swap that empty metadata column in to our mutation table, (d) free the metadata column info from the
// temporary mutation table (which now contains the old ASCII derived states), and then (e) let that mutation
// table go WITHOUT tsk_mutation_table_free(). (It will have pointers to all the same buffers as our own
// mutation table, so we don't want to free it!)
tsk_mutation_table_t temp_mutation_table;

tsk_mutation_table_init(&temp_mutation_table, 0);
tsk_mutation_table_takeset_columns(&temp_mutation_table,
mutation_table.num_rows,
mutation_table.site,
mutation_table.node,
mutation_table.parent,
mutation_table.time,
mutation_table.derived_state,
mutation_table.derived_state_offset,
/* metadata */ NULL,
/* metadata_offset */ NULL);

std::swap(temp_mutation_table.metadata_length, mutation_table.metadata_length);
std::swap(temp_mutation_table.max_metadata_length, mutation_table.max_metadata_length);
std::swap(temp_mutation_table.max_metadata_length_increment, mutation_table.max_metadata_length_increment);
std::swap(temp_mutation_table.metadata, mutation_table.metadata);
std::swap(temp_mutation_table.metadata_offset, mutation_table.metadata_offset);

// WE DO NOT DO:
// tsk_mutation_table_free(&temp_mutation_table);
// INSTEAD WE DO:
tsk_safe_free(temp_mutation_table.metadata); // free the old ASCII derived state data
tsk_safe_free(temp_mutation_table.metadata_offset); // free the offsets for that old data
tsk_safe_free(temp_mutation_table.metadata_schema); // free the schema from tsk_mutation_table_init()
// AND THEN WE JUST LET IT GO OUT OF SCOPE AND DISAPPEAR.

// Put the metadata column in the derived state column; after this, binary derived states
// will be in the derived state column. Empty out the derived state column, which we don't use while simulating;
// we want to free up the buffer rather than having the (perhaps large capacity) buffer hanging around forever.
// See tsk_mutation_table_init for how to initialize an empty metadata column.
tsk_safe_free(mutation_table.derived_state);
tsk_safe_free(mutation_table.derived_state_offset);
mutation_table.derived_state = mutation_table.metadata;
mutation_table.derived_state_offset = mutation_table.metadata_offset;
mutation_table.metadata = (char *) tsk_malloc(1);
mutation_table.metadata_offset = (tsk_size_t *) tsk_calloc(mutation_table.num_rows + 1, sizeof(tsk_size_t));
if (!mutation_table.metadata || !mutation_table.metadata_offset)
EIDOS_TERMINATION << "ERROR (Species::DerivedStatesFromMetadata): allocation failed; you may need to raise the memory limit for SLiM." << EidosTerminate(nullptr);

// Of course the above code will need to be updated if tskit's mutation table implementation changes!
}

Expand Down Expand Up @@ -8880,51 +8848,26 @@ void Species::DerivedStatesToMetadata(tsk_table_collection_t *p_tables)
}

tsk_size_t metadata_size = text_derived_state.size() * sizeof(char);
tsk_size_t metadata_offset_size = (mutation_table.num_rows + 1) * sizeof(tsk_size_t);
char *new_metadata_buffer = (char *)malloc(metadata_size);
if (!new_metadata_buffer)
tsk_size_t *new_metadata_offset_buffer = (tsk_size_t *)malloc(metadata_offset_size);
if (!new_metadata_buffer || !new_metadata_offset_buffer)
EIDOS_TERMINATION << "ERROR (Species::DerivedStatesToMetadata): allocation failed; you may need to raise the memory limit for SLiM." << EidosTerminate(nullptr);

memcpy(new_metadata_buffer, text_derived_state.c_str(), metadata_size);
memcpy(new_metadata_offset_buffer, text_derived_state_offset, metadata_offset_size);


// Now we want to toss any existing metadata column and put this new metadata column data in its place. The
// best way to do this without using (much) private information is to (a) init a new mutation table, (b) use
// tsk_mutation_table_takeset_columns() to set up that table with all our existing columns but with the new
// metadata column, (c) swap its representation of the new metadata column back into our own table, and
// (d) let the temporary mutation table go WITHOUT tsk_mutation_table_free(). (It will have pointers to
// all the same buffers as our own mutation table, so we don't want to free it!)
tsk_mutation_table_t temp_mutation_table;

tsk_mutation_table_init(&temp_mutation_table, 0);
tsk_mutation_table_takeset_columns(&temp_mutation_table,
mutation_table.num_rows,
mutation_table.site,
mutation_table.node,
mutation_table.parent,
mutation_table.time,
mutation_table.derived_state,
mutation_table.derived_state_offset,
/* metadata */ new_metadata_buffer,
/* metadata_offset */ text_derived_state_offset);

std::swap(temp_mutation_table.metadata_length, mutation_table.metadata_length);
std::swap(temp_mutation_table.max_metadata_length, mutation_table.max_metadata_length);
std::swap(temp_mutation_table.max_metadata_length_increment, mutation_table.max_metadata_length_increment);
std::swap(temp_mutation_table.metadata, mutation_table.metadata);
std::swap(temp_mutation_table.metadata_offset, mutation_table.metadata_offset); // identical already, actually

// WE DO NOT DO:
// tsk_mutation_table_free(&temp_mutation_table);
// INSTEAD WE DO:
tsk_safe_free(temp_mutation_table.metadata_schema); // free the schema from tsk_mutation_table_init()
// AND THEN WE JUST LET IT GO OUT OF SCOPE AND DISAPPEAR.

// Finally, swap the derived state column and the metadata column; after this, binary derived states
// will be in the metadata column, and ASCII derived states will be in the derived state column.
std::swap(mutation_table.derived_state_length, mutation_table.metadata_length);
std::swap(mutation_table.max_derived_state_length, mutation_table.max_metadata_length);
std::swap(mutation_table.max_derived_state_length_increment, mutation_table.max_metadata_length_increment);
std::swap(mutation_table.derived_state, mutation_table.metadata);
std::swap(mutation_table.derived_state_offset, mutation_table.metadata_offset);
// Now we want to toss any existing metadata column and put this new metadata column data in its place.
tsk_safe_free(mutation_table.metadata);
tsk_safe_free(mutation_table.metadata_offset);
mutation_table.metadata = mutation_table.derived_state;
mutation_table.metadata_offset = mutation_table.derived_state_offset;
mutation_table.derived_state = new_metadata_buffer;
mutation_table.derived_state_offset = new_metadata_offset_buffer;
for (size_t j = 0; j < mutation_table.num_rows; j++) {
std::cout << mutation_table.derived_state_offset[j] << ", " << mutation_table.metadata_offset[j] << std::endl;
}
}

void Species::AddIndividualsToTable(Individual * const *p_individual, size_t p_num_individuals, tsk_table_collection_t *p_tables, INDIVIDUALS_HASH *p_individuals_hash, tsk_flags_t p_flags)
Expand Down
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