streaming: variants-output surface (variants/variant-windows, min_af/max_af, var_fields) — Wave B of #277

[d-laub]

Part of the write-free StreamingDataset effort — see docs/roadmaps/streaming-dataset.md (Plan 5). Split out of #277.

#277 (output-mode breadth) splits along a hard technical seam into two waves:

• Wave A (streaming: output-mode breadth (annotated/variants, with_len, min_af/max_af, var_fields, jitter) #277, first): with_len, jitter, and with_seqs("annotated") — all reuse the existing streaming window buffer and the fused reconstruct kernels. Plumbing, not new decode.
• Wave B (this issue, right after A): the variants-output surface, which needs new channels decoded into the window buffer (DecodedWindow) per backend.

Scope (Wave B)

Bring StreamingDataset up to the written Dataset's variant-level output surface:

• with_seqs("variants") (RaggedVariants) and with_seqs("variant-windows") (_FlatVariantWindows).
• min_af / max_af filtering. Note: on the written path this is implemented only for variants output (get_variants_flat, _flat_variants.py); haplotype/annotated output raises NotImplementedError (_haps.py:707). Streaming matches that — hence AF lives in Wave B, not A.
• var_fields (custom per-call FORMAT / INFO columns; default ["alt","ilen","start"]).

Why this is the expensive half

The written variants path (get_variants_flat) does not use a reconstruct kernel — it uses assemble_variant_buffers_u8/i32 + gather/compact helpers, consuming per-variant data the current streaming buffer (src/record_stream/transpose.rs::DecodedWindow) does not carry:

• REF allele bytes (ref/ref_offsets) — for RaggedVariants.ref/end and variant-windows.
• AF INFO field — for min_af/max_af.
• dosages / per-call FORMAT fields — for var_fields (Surface genoray SparseVar custom FORMAT fields (Number=G) in Dataset/RaggedVariants, not just dosage #231).
• dataset-global variant ids — streaming's geno_v_idxs are window-local column indices.

fill_decoded_window throws all of this away today; Wave B must extract it per backend (VCF/PGEN INFO/REF decode via genoray DenseChunk; SVAR1/SVAR2 read it from their stores).

Also in scope

• with_seqs("variants") (RaggedVariants) does not clip variants to the region window #202 decision (variants not clipped to the region window on the written path): decide whether streaming reproduces the written bug for parity or we fix both together. Only relevant to variants output, so it lives here.
• Docs + skills/genvarloader/SKILL.md updates for every new knob (per CLAUDE.md's public-API + docs-audit gates).

Parity oracle

Byte-identical vs gvl.write() + Dataset[r, s] under the matching with_seqs(...) / min_af / max_af / var_fields config.

Backends

SVAR1 + VCF + PGEN (the backends merged into streaming). SVAR2 (#298) picks up the same generic code when it merges.