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Fix for memory leak #272

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Merged
joshfactorial merged 2 commits into from
May 3, 2026
Merged

Fix for memory leak #272

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104ea3c
Fix off-by-one in trinucleotide slice and remove stray SNV→all_ins ap…
joshfactorial Apr 28, 2026
c5b896f
Remove orphaned all_ins and all_dels lists from MutationModel
joshfactorial May 3, 2026
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4 changes: 0 additions & 4 deletions neat/models/mutation_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,6 @@ def __init__(self,
self.variant_probs = variant_probs
self.transition_matrix = transition_matrix
self.is_cancer = is_cancer
self.all_dels = []
self.all_ins = []

def get_mutation_type(self, rng: Generator) -> VariantTypes:
"""
Expand Down Expand Up @@ -125,7 +123,6 @@ def generate_snv(self, trinucleotide: Seq, reference_location: int, rng: Generat
# Now pick a random alternate, weighted by the probabilities
alt = rng.choice(ALLOWED_NUCL, p=transition_probs)
temp_snv = SingleNucleotideVariant(reference_location, alt=alt)
self.all_ins.append(temp_snv)
return temp_snv

def generate_insertion(self, location: int, ref: Seq, rng: Generator) -> Insertion:
Expand Down Expand Up @@ -158,5 +155,4 @@ def generate_deletion(self, location: int, rng: Generator) -> Deletion:
# Plus one so we make sure to grab the first base too.
# Note: if we happen to go past the end of the sequence, it will just be shorter.
temp_del = Deletion(location, length)
self.all_dels.append(temp_del)
return temp_del
2 changes: 2 additions & 0 deletions neat/read_simulator/utils/generate_variants.py
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Expand Up @@ -238,6 +238,8 @@ def generate_variants(
location = local_location + ref_start # relative to overall contig
if local_location == 0:
continue
# local_location is the center (mutated) base returned by sample_trinucs;
# shift slice left by 1 so trinuc[0]=5' flank, trinuc[1]=ref base, trinuc[2]=3' flank
trinuc = reference[local_location-1: local_location+2].seq.upper()
disallowed_chars = False
for letter in trinuc:
Expand Down
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