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Support multiple alleles and mutations per site - #1200
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Port the multi-allele support from the tsls copy of the HMM engine. matcher_indexes_alloc now takes optional per-site ancestral state and per-mutation derived state arrays (defaulting to 0 and 1), and sites may carry multiple mutations, with later mutations in tskit order taking precedence. The Python MatcherIndexes wrapper gains an alleles argument that encodes states via the new encode_alleles function.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1200 +/- ##
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+ Coverage 91.55% 91.64% +0.09%
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Files 16 16
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Branches 740 751 +11
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+ Misses 281 280 -1
- Partials 112 114 +2
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Matcher now takes the AlleleMapper and encodes each mutation's derived state in the reference tree sequence to its per-site allele code, so the HMM sees the correct allele for multiallelic sites and for back mutations to the ancestral state. Previously every mutation was treated as derived state 1. Genotype roundtrip checks now include multiallelic inference sites, with new JC69 simulations including samples matched in two groups.
infer_ancestors previously collapsed all derived alleles to code 1, so ancestors at multiallelic sites represented "not ancestral" and were labelled with the first derived allele, and sites whose ancestral allele was absent from the data were silently dropped. It now raises a ValueError naming the site when any ancestor-source genotype is not 0, 1 or missing. Sites with an unknown ancestral allele are skipped with a log message. Multiallelic data remains supported at the matching stage, where samples not used for ancestor generation can carry other alleles. Tests cover the error cases and these matching scenarios (separate sources, sample subsets of one store, simulated data); simulation helpers now default to biallelic mutations.
jeromekelleher
enabled auto-merge
October 16, 2026 12:44
jeromekelleher
disabled auto-merge
October 16, 2026 12:44
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Closes #1186