0.8.0

v0.8.0 (2025-02-05)

Feat

• sequence annotations

v0.7.3 (2025-01-27)

Feat

• allow subset_to() to accept boolean masks and polars Series
• allow subset_to() to accept boolean masks and polars Series

Fix

• add test for subset_to
• add test for subset_to
• update tests to match internal API changes
• update tests to match internal API changes
• bug in mark_keep_variants with spanning deletions.

v0.7.2 (2025-01-26)

Fix

• change loop order to only open files once.
• respect memory limits when writing bigwig data.
• online docs notebook syntax highlightning
• better docs.

v0.7.1 (2025-01-17)

Fix

• bump version
• scalar dataset indexing, region_indices order, updated docs, hotfixes

v0.7.0 (2025-01-17)

Feat

• indexing matches input bed file. make sel() a private method pending better API design. fix: pass tests for indexing and separate indexing and subsetting logic into DatasetIndexer.
• write input regions to disk with a column mapping each to a row in the sorted dataset regions

Fix

• passing tests
• passing tests
• passing tests

v0.6.4 (2024-12-16)

Fix

• update rust dependencies.

v0.6.3 (2024-12-16)

Fix

• unintended torch requirements

v0.6.2 (2024-12-16)

Fix

• update version
• StratifiedSampler requires torch. fix: remove deprecated conda env files.

v0.6.1 (2024-11-25)

Fix

• handle empty genotypes during gvl write. fix: PgenGenos sample_idx should be sorted when compared to current sample_idx.

v0.6.0 (2024-09-03)

Feat

• bump version
• geuvadis tutorial.
• tutorial notebook, pooch dependency.

Fix

• update available tracks after writing transformed ones to disk.

v0.5.6 (2024-08-07)

Fix

• bump version
• offsets can overflow int32, use int64 instead.

v0.5.5 (2024-08-02)

Fix

• make Records.vars_in_range... functions fallible by returning None instead of "empty" RecordInfo instances. This fixes downstream behavior of the Variants.read.. methods when there are no variants in the query. feat: when reading VCFs for the first time and no index is found, try to index them first before raising an error. fix: better docstrings on attributes of private API.
• add build number to replace yanked release

v0.5.4 (2024-07-05)

Fix

• fix breaking changes from polars 1.0
• fix breaking changes from polars 1.0

v0.5.3 (2024-07-05)

Fix

• fix breaking changes from polars 1.0
• fix breaking changes from polars 1.0

v0.5.2 (2024-07-05)

Fix

• typo in pyproject causing dependencies to be ignored.
• typo in pyproject causing dependencies to be ignored.

v0.5.1 (2024-06-29)

Feat

• prep for readthedocs
• prepare for online documentation.

Fix

• add favicon
• documentation formatting
• rtd config
• rtd config
• rtd config
• rtd config
• rtd config
• rtd config
• rtd config
• readthedocs dependencies
• readthedocs config
• readthedocs config
• readthedocs config
• readthedocs config
• readthedocs config
• readthedocs config

v0.5.0 (2024-06-13)

Feat

• bump version
• multiprocess reading of genotypes, both VCF and PGEN. fix: bug in reading genotypes from PGEN

v0.4.1 (2024-06-11)

Fix

• bump version
• got number of regions from wrong array in get_reference

v0.4.0 (2024-06-05)

Feat

• deprecate old loader, worse performance. reorganize code.

Fix

• better documentation in README. feat!: rename write_transformed_tracks to write_transformed_track. feat: more ergonomic indexing.

v0.3.3 (2024-06-01)

Fix

• bump version
• wrong max_ends from SparseGenotypes.from_dense_with_length due to data races/incorrect parallel semantics for numba
• diffs need to be clipped and negated when computing shifts

Perf

• pad haplotypes on-the-fly to avoid extra copying of reference subsequences

v0.3.2 (2024-04-29)

Feat

• can convert Records back to a polars DataFrame with minimal copying via conversion of VLenAlleles to pyarrow buffers
• make open_with_settings the standard open function. fix: recognize .bgz extension for fasta files

Fix

• remove dynamic versioning table
• move cli to main feat: generalize Variants to automatically identify whether vcf or pgen is passed
• move cli to script in python source directory, maturin limitation?
• wrong implementation of heuristic for extending genotypes.

Perf

• faster sparsifying genotypes. feat: log level for cli. fix: clip missing lengths for appropriate end extension.

v0.3.1 (2024-04-16)

Feat

• benchmark interval decompression on cpu with numba vs. cpu with taichi vs. gpu with taichi
• optionally decompress intervals to tracks on gpu
• initial support for stranded regions
• option to cache fasta files as numpy arrays.
• implement BigWig intervals as Rust extension.
• finishing touches on multi-track implementation. Block is cryptic issue where writing genotypes is somehow preventing joblib from launching new processes.
• stop overwriting by default, add option.
• transforms directly on tracks. feat: intervals as array of structs for better data locality.
• let extra tracks get added via paths
• let extra tracks get added via paths
• initial support for indels in tracks and WIP on also returning auxiliary genome wide tracks.
• initial sparse genos -> haplotypes and sparse hap diffs.
• wip sparse genotypes.
• properties for getting haplotypes, references, or tracks only.
• properties for getting haplotypes, references, or tracks only.
• encourage num_workers <= 1 with GVL dataloader.
• freeze gvl.Dataset to prevent user from accidentally introducing invalid states. feat: warn if any query contigs have either no variatns or intervals associated with them.
• warn instead of error when no reference passed and genos present.
• disable overwriting by default, have no args be help.
• also report number of samples.
• add .from_table constructor for BigWigs.
• move CLI to script, include in package.
• use a table to specify bigwigs instead. fix: jittering.
• add script to write datasets to disk.
• more quality of life improvements. relax dependency version constraints.
• with_seed method
• quality of life methods for subsetting and converting to dataloaders.
• torch convenience functions fix: ensure genotypes and intervals written in sorted order wrt the BED file.
• pre-computed implementation.

Fix

• dependency typo
• remove taichi interval to track implementation since it did not improve performance, even on GPU
• need to subset arrays to be reverse complemented
• change argument order of subset_to to match the rest of the API. fix: simplify subset implementation.
• remove python 3.10 type hints
• dimension order on subsets.
• make variant indices absolute on write.
• sparse genotypes layout
• sparse genotypes layout
• wrong layout out genotypes and wrong max ends computation.
• ragged array layouts for correct concatenation when writing datasets one contig at a time.
• bug where init_intervals would not initialize all available tracks.
• track_to_intervals had wrong n_intervals and thus, wrong offsets.
• track_to_intervals had wrong n_intervals and thus, wrong offsets.
• bug in computing max ends.
• match serde for genome tracks.
• bug in open state management.
• bug when writing genotypes where the chromosome of the requested regions is not present in the VCF.
• bug getting intersection of samples available.
• bug getting intersection of samples available.
• sum wrong axis in adjust multi index.
• make GVLDataset getitem API match torch Dataset API (i.e. use raveled index)
• QOL improvements.
• incorrect genotypes returned from VCF when queries have overlapping ranges.
• wrong shape.
• wrong shape.

Refactor

• move construct virtual data to loader so utils import faster.
• move construct virtual data to loader so utils import faster.
• rename util to utils.
• rename util to utils.
• move write under dataset directory. perf?: move indexing operations into numba.
• move cli to script outside package, faster help message.
• break up dataset implementation into smaller files. refactor!: condense with_ methods into single with_settings() methods. feat: sel() and isel() methods for eager retrieval by sample and region.

Perf

• when opening witih settings and providing a reference, but return_sequences is false, don't load the reference into memory.

v0.3.0 (2024-03-15)

Feat

• write ZarrTracks in smaller chunks.
• write ZarrTracks in smaller chunks.

Fix

• remove wip vidx feature.
• relax numba version constraint
• rounding issues for setting fixed lengths on BED regions.
• more informative vcf record progress bar.

v0.3.0rc6 (2024-03-11)

Feat

• improve record query performance by allowing nearest_nonoverlapping index adjustment to be computed on-the-fly in the weighted activity selection algorithm and thus also benefit from early stopping.
• more descriptive progress bar for constructing ZarrGenos from another file.
• add progress bar for reading VCF records.

Fix

• pylance update, catch possibly unbound variables.
• instead of failing, raise warning when encountering non-SNP, non-INDEL variants and skip them.

v0.3.0rc5 (2024-03-04)

Fix

• more descriptive pbar when writing ZarrTracks from another reader.
• BigWigs, only keep contigs that are shared across all bigwigs.
• better error messages and catching cases for non-SNP, non-INDEL variants.
• avoid segfault caused when a TensorStore is forked to new processes.
• make ZarrTracks implement Reader protocol. feat: add NumpyGenos for in-memory representation. feat: better ZarrGenos.from_recs_genos progress bar.

v0.3.0rc4 (2024-02-29)

Fix

• naming of .ends.gvl.arrow to .gvl.ends.arrow so file suffix parsing works correctly.

v0.3.0rc3 (2024-02-29)

v0.3.0rc2 (2024-02-29)

Fix

• remove pyd4 dependency, had unspectacular performance.

v0.3.0-rc.1 (2024-02-28)

Feat

• add ZarrTracks for much faster performance than D4.
• finish deprecating parallel GVL...