Fix for memory leak#272
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…pend sample_trinucs returns the center (mutated) position, but the trinuc slice was starting at that position rather than one before it, so trinuc[1] was the 3' context base instead of the ref base. generate_snv uses trinuc[1] as the ref base for transition-matrix lookup and REF==ALT zeroing, so the wrong base was being consulted — Keshav's zeroing fix in #267 only worked when reference[pos] == reference[pos+1]. Fix: shift the slice to reference[local_location-1: local_location+2] so trinuc[0]=5' flank, trinuc[1]=ref base, trinuc[2]=3' flank. Also remove the dead self.all_ins.append(temp_snv) in generate_snv; SNVs were being accumulated in MutationModel.all_ins (a list that is never read) rather than nowhere, a copy-paste artifact from generate_deletion. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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These lists were never read anywhere; ContigVariants has its own independent all_ins/all_dels used for overlap detection. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Found some lists that were being written, but the code was refactored so that the lists were never actually used. Could cause a small memory leak, so they were removed.