Fix merge -m none incorrectly merging records with different allele sets#2521
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix merge -m none incorrectly merging records with different allele sets#2521sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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…ele sets (samtools#2498) When using `bcftools merge -m none`, records at the same position with overlapping but non-identical allele sets (e.g., ALT=T vs ALT=T,G) were incorrectly merged because types_compatible() only checked that the new record's alleles were a subset of the existing merged alleles. Add an explicit check that the number of alleles must match exactly in COLLAPSE_NONE mode, ensuring only records with identical allele sets are merged together.
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Summary
types_compatible(), COLLAPSE_NONE mode checked if the incoming record's alleles were a subset of the merged alleles, but not the reverse — a record with ALT=T would merge with ALT=T,Grec->n_allele != maux->nalscheck to require exact allele count matchFixes #2498
Test plan
bcftools merge -m nonekeeps records with different ALT sets separate