feat(cli): replace --skip-symbolic-alts with composable --no-symbolic / --no-breakend#53
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… ILEN) Breakend (BND) ALTs in mate-pair / single-breakend notation (e.g. `G[chr2:321[`, `.TGCA`) are a distinct VCF 4.x ALT class from symbolic `<...>` alleles, so `is_symbolic` did not flag them. But like symbolic alleles they are not expandable into nucleotides — the bracket/colon/ position bytes corrupt personalized DNA buffers in haplotype consumers. Previously a breakend slipped past every guard: `symbolic_ilen` computed the literal `len(ALT) - len(REF)`, so it masqueraded as a large insertion, evaded `~is_imprecise`, and reached consumers like genvarloader. - Add public `is_breakend` expression (VCF §5.4 grammar). - `symbolic_ilen` now returns null for breakend ALTs, so they are also `is_imprecise` and excluded from `is_snp`/`is_indel`. Flows through both the VCF and PGEN index-build paths. - Document the haplotype-safe filter `~is_symbolic & ~is_breakend` in SKILL.md (required for public-API changes). - Add a breakend record to the `symbolic` test fixture and extend the oracle/persisted-index tests to cover the path on generated data. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
… predicates Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…reakend Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The setter previously mutated only _filter, allowing a mismatched (filter, pl_filter) pair that the constructor forbids. It now accepts a (filter, pl_filter) tuple (or None to clear both), validates the both-or-neither invariant via a shared _check_filter_pair helper, and invalidates the in-memory index. Getter still returns the callable. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
genoray write --skip-symbolic-altsflag with two independent, composable flags--no-symbolicand--no-breakend, so users can drop un-injectable ALT classes (symbolic alleles like<DEL>, breakends likeG[chr1:500[) independently or together._record_is_symbolic/_record_is_breakendtogenoray/exprs.pythat mirror the existingis_symbolic/is_breakendpolars exprs (sharing_BND_PATTERN), keeping the cyvcf2 record callable and the polars index filter in parity.(record callable, polars expr)for the VCF path (both required, or neither) and a single polars expr for PGEN.Test Plan
pixi run test— 347 passed, 16 xfailedruff check+ruff format --checkcleangenoray write --helpshows--no-symbolic/--no-breakend, no--skip-symbolic-altsor--no-no-*--no-breakend/ combined--no-symbolic --no-breakendacross VCF, plus--no-breakendPGEN🤖 Generated with Claude Code