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bug fixes in add_mutation_metadata_tables #434

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bug fixes in add_mutation_metadata_tables #434

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3bc083f
bug fixes in add_mutation_metadata_tables
jeffspence Aug 19, 2026
032655d
missing word in convert_alleles docstring
jeffspence Aug 20, 2026
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52 changes: 29 additions & 23 deletions pyslim/methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -450,28 +450,34 @@ def add_mutation_metadata_tables(tables, mutation_type=0, remove_unused=False):
for mut in tables.mutations
for j in mut.derived_state.split(",")
]
mut_ids.sort()
mut_ids = np.array(mut_ids, dtype="int") # floors times
# remove duplicate IDs, keeping the last (most recent)
keep = np.full(len(mut_ids), True, dtype="bool")
keep[np.where(np.diff(mut_ids[:, 0]) == 0)[0]] = False
mut_ids = mut_ids[keep, :]
mut_ids[:, 1] = slim_time(
tables, mut_ids[:, 1], stage="late", ts_metadata=ts_metadata
)
# this assumes mutations were added in late(), which is what SLiM does
ts_metadata["SLiM_mutation_list"].extend(
[
default_slim_metadata(
"mutation_list_entry",
mutation_id=int(j),
mutation_type=mutation_type,
slim_time=int(t),
)
for j, t in mut_ids
if j not in existing_muts
]
)

# Only do things if there are mutations
# avoids an edge case where numpy indexing is out of bounds
# because empty lists create numpy arrays with only one dimension
if len(mut_ids) > 0:
mut_ids.sort()
mut_ids = np.array(mut_ids, dtype="int") # floors times
# remove duplicate IDs, keeping the last (most recent)
keep = np.full(len(mut_ids), True, dtype="bool")
keep[np.where(np.diff(mut_ids[:, 0]) == 0)[0]] = False
mut_ids = mut_ids[keep, :]
mut_ids[:, 1] = slim_time(
tables, mut_ids[:, 1], stage="late", ts_metadata=ts_metadata
)
# this assumes mutations were added in late(), which is what SLiM does
ts_metadata["SLiM_mutation_list"].extend(
[
default_slim_metadata(
"mutation_list_entry",
num_traits=len(ts_metadata["SLiM"]["traits"]),
mutation_id=int(j),
mutation_type=mutation_type,
slim_time=int(t),
)
for j, t in mut_ids
if j not in existing_muts
]
)
if remove_unused and len(mut_ids) < len(ts_metadata["SLiM_mutation_list"]):
ts_metadata["SLiM_mutation_list"] = [
x for x in ts_metadata["SLiM_mutation_list"] if x["mutation_id"] in mut_ids
Expand All @@ -486,7 +492,7 @@ def convert_alleles(ts):
have "" (the empty string) for the ancestral state at each site; this method
will replace this with the corresponding nucleotide from the reference sequence.
For mutations, SLiM records the 'derived state' as a SLiM mutation ID; this
method will this with the nucleotide from the mutation's metadata.
method will replace this with the nucleotide from the mutation's metadata.

This operation is not reversible: since SLiM mutation IDs are lost, the tree
sequence will not be able to be read back into SLiM.
Expand Down