Skip to content

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.10.0] -- 2026-09-05

  • refget: writers now take an exclusive store lock and commit only their own changes; concurrent imports no longer lose collections, and a stale handle no longer resurrects removed rows
  • refget: all index, manifest, alias, and sequence files are written atomically (write-temp then rename)
  • refget: fix cleanup after a failed import deleting pre-existing sequences on a reopened store
  • refget: orphan-sequence GC is linear instead of quadratic; large removals finish in seconds instead of hours
  • refget: export_fasta and get_sequence_by_name use the collection's own names and descriptions #270
  • refget: add ImportReport with per-run counters (n_sequences_written, n_sequences_deduped, n_collections_new); add_sequence_collections_from_fastas now returns it
  • refget: add import-time collection aliases (--collection-alias ns:alias, FastaImportOptions::collection_alias, Python collection_alias=)
  • refget: add logical_sequence_bytes to the store manifest; rename total_disk_size() to logical_sequence_bytes()
  • refget: rename StoreStats fields n_sequences_loaded/n_collections_loaded to n_sequences_in_memory/n_collections_in_memory across Rust, Python, R, and Node
  • refget: encoded stores accept pre-packed sequences at insert time
  • cli: add gtars refget export (-c <digest|ns:alias>, -w 0 for unwrapped FASTA, .gz output)
  • overlaprs: remove unused MultiChromOverlapperError
  • wasm: fix encodedByteRange return type in typings

[0.9.1] -- 2026-06-17

Point release of refget 0.9.1, python 0.9.2, R 0.9.2, node 0.7.1, wasm 0.9.1 #268. - refget: unify remote on-demand sequence retrieval into three flows: get_substring (byte-range read), stream_sequence (streaming reader), load_sequence (download and cache) - refget: bulk substring reads on a remote-only sequence download and cache the .seq once instead of one request per range - python, R, node: expose stream_sequence, load_sequence, and load_all_sequences; node no longer auto-downloads whole chromosomes - wasm: add RemoteRefgetStore JS layer (HTTP byte-range + OPFS caching) via @databio/gtars/remote

[0.9.0] -- 2026-06-15

  • add gtars-vrs crate: GA4GH VRS allele identifiers from VCF/HGVS, with an HGVS parser, allele normalization, and transcript-anchored mapping
  • add Node.js bindings (gtars-node)
  • refget: on-disk sequence store overhaul; add binary transcript store and coordinate mapper
  • genomicdist: add binary FASTA (.fab) format with zero-copy mmap access; add stranded region-set operations
  • uniwig: add BAM QC tooling
  • overlaprs: overlap-engine rewrite
  • expanded WASM and Python bindings
  • correctness fixes across vrs, refget, bamqc, and the Python HGVS AST

[0.8.0] -- 2026-03-19

  • genomicdist: port of genomic distributions #231, bug fixes #244
  • uniwig: add streaming implementation alongside the batch parallel one #236
  • refget: RefgetStore updates #237
  • add gtars-lola crate; IGD supports an in-memory database #242
  • expose more functionality via Python #241

[0.7.0] -- 2026-02-24

  • update all crates to Rust edition 2024
  • refget: add sequence and collection aliases, ancillary digests, seqcol comparison, and FHR metadata; sequences can exist independently of a collection
  • refget: add streaming FASTA digest computation in WASM
  • uniwig: fix off-by-one errors; add variable-step format
  • refactor R bindings; RefgetStore uses ExternalPtr so R garbage collection works
  • RegionSet returns an error instead of panicking on bad input

[0.6.0] -- 2026-01-26

  • refget: add FAI (FASTA index) computation and metadata storage
  • refget: add remote-access RefgetStore with lazy loading and caching; SequenceRecord is now an enum (Stub vs Full)
  • refget: add on_disk(), in_memory(), load_remote() constructors and export methods

[0.5.3] -- 2026-01-21

  • remove reqwest dependency from gtars-core
  • merge the gdrs package into gtars
  • genomicdist: add bed classifier

[0.5.2] -- 2025-11-04

  • switch overlap operations to MultiChromOverlapper
  • genomicdist: more tests, fix region distribution plot, fix function naming in wasm bindings
  • load/write functions accept AsRef<Path>

[0.5.1] -- 2025-10-08

  • introduce web assembly bindings
  • introduce R bindings

[0.5.0] -- 2025-09-25

  • converted the codebase into a workspace with multiple crates

[0.4.0] -- 2025-09-10

  • added get_max_end_per_chr and nucleotides_length methods to RegionSet

[0.3.0] -- 2025-07-30

  • move digests functionality to refget
  • add RefgetStore to refget and its associated python bindings
  • integrate support for bits + backend types for tokenizers (AIList or BITS)
  • reworked the tokenization CLI to support the new bits and backend options

[0.2.5] -- 2025-04-06

  • Rework tokenizer API to be more consistent with the HuggingFace tokenizers API.
  • Updates to RegionSet to improve performance and usability.
  • Added file_digest function to RegionSet struct
  • Fixed reqwest error in R bindings
  • Fixed #107

[0.2.4] -- 2025-03-05

  • Attempt to fix failing python bindings in CI linux #104

[0.2.3] -- 2025-03-05

  • Improved RegionSet, by adding a multiple new methods: to_bed, to_bed_gz, to_bigbed, identifier(), and others.
  • Fixed allowed fasta_digest to accept Path or bytes #93

[0.2.2] -- 2025-02-18

[0.2.1] -- 2025-02-11

  • allow comments at the beginning of fragment files
  • bump bigtools to 0.5.5, fixing #74 and #77

[0.2.0] -- 2025-01-13

  • add position shift workflow for bam to bw (was previously added for bam to bed)
  • add scaling argument for bam to bw workflow #53
  • fix accumulation issue for bam workflow #56
  • fix wiggle file (core) beginning at 0 #43
  • fix npy file (end) using start instead of end #61
  • force zoom to 1 for bed/narrowPeak to bw #34
  • fix IGD overlap issue #45
  • add ga4gh refget digest functionality #58
  • fix wig and npy inconsistency #64
  • fix narrowPeak to bw zoom #34
  • fix bed to bw fileheader consistency issue #52
  • change npy metadata file structure #65

[0.1.2]

  • add position shift workflow for bam to bw (was previously added for bam to bed)
  • add scaling argument for bam to bw workflow #53
  • fix accumulation issue for bam workflow #56
  • fix wiggle file (core) beginning at 0 #43
  • fix npy file (end) using start instead of end #61
  • force zoom to 1 for bed/narrowPeak to bw #34
  • fix IGD overlap issue #45
  • add ga4gh refget digest functionality #58

[0.1.1] -- 2024-12-03

  • hot fix for broken python bindings; remove IGD from the python bindings for now

[0.1.0] -- 2024-12-03

  • Rust implementation of uniwig that expands on the C++ version
  • Uniwig now accepts a single sorted .bed file, .narrowPeak file, or .bam file.
  • Outputs now include .wig, .npy, .bedGraph, and .bw
  • Accumulations can now be counted via .narrowPeak scoring
  • Rust implementation of igd ported from the C version (experimental).
  • Region scoring matrix calculation for region clustering
  • Fragment file splitter for pseudobulking

[0.0.15] -- 2024-07-29

  • added meta tokenization tools and a new MetaTokenizer struct that can be used to tokenize regions using the meta-token strategy.
  • added some annotations to the pyo3 #[pyclass] and #[pymethods] attributes to make the python bindings more readable.

[0.0.14] -- 2024-06-11

  • renamed repository to gtars to better reflect the project's goals.

[0.0.13] -- 2024-06-03

  • implemented a fragment file tokenizer that will generate .gtok files directly from fragments.tsv.gz files.
  • fix an off-by-one error in the region-to-id maps in the Universe structs. This was leading to critical bugs in our models.

[0.0.12] -- 2024-05-28

  • optimize creation of PyRegionSet to reduce expensive cloning of Universe structs.

[0.0.11] -- 2024-05-22

  • redesigned API for the tokenizers to better emulate the huggingface tokenizers API.
  • implemented new traits for tokenizers to allow for more flexibility when creating new tokenizers.
  • bumped the version pyo3 to 0.21.0
  • added rust-numpy dependency to the python bindings for exporting tokenized regions as numpy arrays.
  • overall stability improvements to the tokenizers and the python bindings.

[0.0.10] -- 2024-01-24

  • update file format specifications

[0.0.9] -- 2024-01-22

  • start working on the concept of a .gtok file-format to store tokenized regions
  • added basic readers and writers for this format

[0.0.8] -- 2024-01-17

  • add a new ids_as_strs getter to the TokenizedRegionSet struct so that we can get the ids as strings quickly, this is meant mostly for interface with geniml.

[0.0.7] -- 2023-11-30

  • move things around based on rust club feedback

[0.0.6] -- 2024-02-20

  • update python bindings to support the module/submodule structure (https://github.com/PyO3/pyo3/issues/759#issuecomment-1828431711)
  • change name of some submodules
  • remove consts submodule, just add to base
  • expose a __version__ attribute in the python bindings

[0.0.5] -- 2024-02-19

  • add many "core utils"
  • move gtokenizers into this package inside gtars::tokenizers
  • create tokenize cli
  • add tests for core utils and tokenizers
  • RegionSet is now backed by a polars DataFrame
  • new python bindings for core utils and tokenizers

[0.0.4] -- 2023-11-06

  • add type annotations to the python bindings

[0.0.3] -- 2023-11-06

  • work on python bindings initialization

[0.0.2] -- 2023-09-20

  • prepare for first release

[0.0.1] -- 2023-08-15

  • initial setup of repository
  • two main wrappers: 1) wrapper binary crate, and 2) wrapper library crate
  • gtars can be used as a library crate. or as a command line tool