CHANGES.md

Changelog

Unreleased

New features

Enhancements

• silent argument to query_* methods.
• CLI query returns meaningful ERROR if no seq/tracks are found.

Bug fixes

• Fix MomicsDataset and generator.

v0.4.0

Date: 2024-10-25

API changes

• MultiRangeQuery -> MomicsQuery.
• manifest method to output the whole configuration of a Momics instance.
• consolidate method to consolidate a Momics repository.
• No submodules are imported in __init__.py anymore.
• All export functions are now Momics methods.
• All ingestion methods for Momics now start with ingest_*.

New features

• aggregate submodule to merge dictionaries of partial coverage tracks (over pyranges) into genome-wide tracks.
• Relatively basic ChromNN CNN TensorFlow model.
• MomicsDataset class to pass data to TensorFlow models.
• MomicsStreamer class to stream data from Momics repositories.
• Momics can ingest pyranges objects to store genomic features.
• Sequences, features and tracks can be extracted from a Momics repository.

Enhancements

• CLI is now partially based on cloup to improve user experience.
• seq(label = "...) now returns the sequence for an entire chromosome.
• tracks(label = "...) now returns the genome-wide track.
• MomicsQuery queries now rely on pyranges for range queries.
• MomicsQuery queries can extract only a subset of the tracks.
• add_track and remove methods for Momics class.
• to_npz and to_json methods for MomicsQuery class.

Maintenance

• Support jupyter notebooks in documentation.
• Add changelog.
• Improve docs.
• Logging system updates.
• CLI updates.
• Add codecov support.

Bug fixes

• Ensure that queries are done per chromosome, even if provided ranges are stranded.
• All ranges are now 0-based half-open intervals, as in pyranges and BED files.
• Parallelization for queries only relies on TileDB internal system.
• Filters used in Momics tables.
• Removal of Azure-hosted repositories.

v0.3.0

Date: 2024-09-26

New features

• MultiRangeQuery relies on pybedtools for range queries.
• Queries support both coordinates and multi-loci queries.
• Added MultiRangeQuery class for queries.
• New bins method for Momics.
• Repositories can ingest fasta files.
• Added export submodule.
• Added MomicsConfig class to manage cloud configuration settings.
• Added Click-based CLI commands.

Enhancements

• Improve query filters.
• CLI commands have mutli-threading options.

Maintenance

• Added ruff support.
• Changed doc theme.
• Added support for autoapi in documentation.
• Improved tests coverage.

Bug fixes

• Fixed broken use of single-file temporary store in create_from_unordered.
• Added heuristic in pairix cload to prevent excessively large chunks. #92
• Added extra checks in cload pairix and cload tabix. #62, #75

v0.2.0

Date: 2024-07-31

Enhancements

• Implement Momics class.

v0.1.0

Date: 2024-07-29

Enhancements

• Initial prototype.