v0.4.1

Bug fixes:

• Fix bug introduced in the last release in select and select_* query interval semantics. Results of select are now consistent with the query interval being interpreted as half-open, closed on the left.

v0.4.0

API changes:

• New strand-aware directionality options for closest() via direction_col #129.
• New index-based range query selectors on single bioframes to complement select() #128:
  • select_mask() returns boolean indices corresponding to intervals that overlap the query region
  • select_indices() returns integer indices corresponding to intervals that overlap the query region
  • select_labels() returns pandas label indices corresponding to intervals that overlap the query region

Bug fixes:

• Import fixes in sandbox
• Relax bioframe validator to permit using same column as start and end (e.g. point variants).

v0.3.3

Bug fixes

• fixed a couple functions returning an error instance instead of raising
• fetch_mrna link fixed

v0.3.2

• fixes error in is_contained
• tutorial updates

v0.3.1

API changes:

• bioframe.sort_bedframe does not append columns or modify their dtypes.

v0.3.0

Maintenance

• Drop support for Python 3.6, add support for 3.9
• Pandas dependency bumped to 1.3
• Lots of new documentation

Conceptual changes

We formulated strict definitions for genomic intervals, dataframes, and their various properties. All bioframe functions are expected to adhere to these definitions.

API changes

Reorganize modules

• ops - operations on genomic interval dataframes
• extras - miscellaneous operations, most involving
  genomic sequences and gene annotations
• vis - visualizations of genomic interval dataframes
• core.arrops - operations on genomic interval arrays
• core.checks - tests for definitions of genomic interval dataframes
• core.construction - construction and sanitization of genomic interval dataframes
• core.specs - specifications for the implementation of genomic intervals using pandas dataframes
  (i.e. column names, datatypes, etc)
• core.stringops - operations on genomic interval strings
• io.fileops - I/O on common file formats for genomic data
• io.schemas - schemas for standard tabular formats for genomic data storage
• io.resources - interfaces to popular online genomic data resources

New functions

• extras.pair_by_distance, ops.sort_bedframe, ops.assign_view, dataframe constructors

Existing functions

• expand: take negative values and fractional values
• overlap: change default suffixes, keep_order=True
• subtract: add return_index and keep_order

Enable pd.NA for missing values, typecasting

Data additions

• add schemas for bedpe, gap, UCSCmRNA, pgsnp
• add tables with curated detailed genome assembly information

Miscellaneous

• frac_gc is faster now

v0.2.0

API changes

• read_chromsizes and fetch_chromsizes: add new as_bed parameter.
• read_chromsizes and fetch_chromsizes: revert to filtering chromosome names by default, but clearly expose filter_chroms kwarg.

Bug fixes

• Fixed bioframe.split
• Restored frac_genome_coverage

v0.1.0

First beta release.

What's new

• New extensive dataframe genomic interval arithmetic toolsuite.
• Improved region handling and region querying functions.
• Documentation!

Maintenance

• Dropped Python 2 support
• Refactoring of various genome operations and resources.
• Improved testing and linting

v0.1.0-rc1

Testing publishing to PyPI with Github Actions.

v0.0.12-doi

Zenodo.