pangenome-range

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Format goals and current research candidate ​

File-format v1 (PNGRNG01 with PNGRGN01 record-preserving payloads) is the only current format. Rust and TypeScript implement it from the normative File Format v1, share one golden conformance matrix, and have completed a whole-source build plus real HTTP-range smoke. The project is still unreleased and the format is not stable.

Candidate work should pursue and measure:

  • very few range requests and serial dependency rounds;
  • small independently cacheable bootstrap metadata;
  • low read amplification and duplicate-byte retrieval;
  • minimal expansion relative to the same source GBZ;
  • independently decompressible regions;
  • unsigned 64-bit offsets and lengths;
  • deterministic, bounded-memory construction;
  • browser decoding without native bindings;
  • immutable static-object hosting without a custom query backend;
  • complete node, edge, reference, coordinate, multiplicity, weight, and provenance semantics;
  • deterministic validation and corruption detection;
  • explicit bounds for collapsed graph regions and malformed inputs.

Open research questions include compressed-record sharing, acceptable archive expansion, optional sidecars, and archive-wide construction/query cost for named identity. Each answer belongs in a named, correctness-gated experiment.

Optional named source-path membership is now a registered v1 feature. Direct bounded construction, persistent-cache reuse, Rust validation, and the public TypeScript API are implemented. Fixed membership-directory pages scale with graph directory pages, not a root-wide tile list. The feature preserves tile-local GBWT source identity; it does not redefine anonymous graph-query traversals as globally stitchable samples. Whole-HPRC construction remains unmeasured and 1000G remains an explicit memory-safety exclusion, not an inferred result. Bounded rice/HPRC pilots do not establish archive-wide identity storage overhead.

While the project remains pre-release, an incompatible format change replaces v1 in place and regenerates all fixtures. It does not add a compatibility decoder or reinterpret an old research object. Package semantic versions remain independent of the on-disk v1 identifier.