Solving VCF-related issues.#267
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joshfactorial
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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>
joshfactorial
added a commit
that referenced
this pull request
May 3, 2026
…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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Fixes and tests for issues #256 and #266.