4.4.0

Documentation

• Assert inside the registration in the README examples (#89) (088839c)

Features

• Find fgumi and fgbio variant reviews with bedspec.ext.captainslog (#90) (626a9fc)

4.3.0

Features

• Add bedspec.ext.captainslog for captainslog's interval-like records (#88) (b39f30a)

4.2.1

Build

• Pin typeline, pybgzf, and superintervals to one series (#86) (8b563c7)

Continuous Integration

• Bump the github-actions group with 3 updates (#83) (f1415c9)
• Bump the python-dev group with 2 updates (#85) (145d060)
• Bump superintervals from 1.0.2 to 1.0.3 in the python-runtime group across 1 directory (#84) (42c4b75)
• Bump to 4.2.1 (#87) (4236177)

4.2.0

Continuous Integration

• Bump basedpyright (#78) (e316a65)
• Bump the github-actions group with 2 updates (#77) (0e2ca7f)
• Bump pybgzf from 0.1.2 to 0.2.0 in the python-runtime group (#76) (7422e95)
• Bump to 4.2.0 (#82) (8290ffb)

Documentation

• Highlight README examples as python and test them with sybil (#74) (92cf214)

Features

• Add thick_territory() to BED9 and BED12 records (#72) (3c768d2)
• Register how detectors and territories find other records' spans (#75) (0cbc9af)
• Add a sort extra and run every readme example in ci (#81) (d86cd41)

Performance

• Make isinstance checks against BedLike cheap (#79) (49c4518)

4.1.2

Build

• Require typeline 2.4.2 (#70) (63ea68d)

Continuous Integration

• Bump the python-dev group with 2 updates (#69) (10a7e8d)
• Bump to 4.1.2 (#71) (d219aa0)

4.1.1

Build

• Require typeline 2.4.0 (#67) (69b0736)

Continuous Integration

• Bump to 4.1.1 (#68) (79c183a)

4.1.0

Continuous Integration

• Bump to 4.1.0 (#66) (226727b)

Features

• Take the BGZF file suffixes from pybgzf (#65) (8ace9eb)

Refactor

• Drop a write_through call pybgzf already makes (#64) (b340543)

4.0.0

Breaking

• Add Territory, return it from territory(), and use BED12 blocks (#61) (aec489c)
  • record.territory() returns a Territory instead of an iterator of spans. Use record.spans() wherever each piece or its strand matters.
  • A custom record overrides spans() instead of territory(), which is now final; defining territory() raises a TypeError naming spans().
  • A Bed12 is its blocks: its territory holds only its exons, and a query touching only an intron no longer finds it in TreeDetector or TabixDetector. To find a Bed12 by its whole extent, add it as a Bed6.
• bedspec now requires typeline 2.3.0 or newer.

Features

• Territory, an immutable set of bases with |, &, -, .length, contains and in (#61)

Build

• Require typeline 2.3.0 (#62) (aa5d84b)

Continuous Integration

• Bump ruff from 0.16.8 to 0.16.9 in the python-dev group (#60) (5a29a63)
• Bump to 4.0.0 (#63) (6f7dc37)

3.0.0

Breaking

• Rename OverlapDetector to TreeDetector (#53) (cab4827)
• Index every span of a feature's territory (#58) (1623c6e)
  • TreeDetector accepts Bed2 and BEDPE, and a BEDPE is found by either end.
  • enclosed_by yields a feature only when every span of its territory is inside the query.
  • Iterating a TreeDetector yields features in the order they were added, instead of grouped by reference.
• bedspec now requires pybgzf 0.1.1, superintervals 1.0.2 and typeline 2.2.0 or newer.

Build

• Require superintervals 1.0.2 and use its has_overlaps (#57) (9243809)

Continuous Integration

• Run the tests on pull requests from forks (#55) (7313d98)
• Bump to 3.0.0 (#59) (1447392)

Features

• Write indexed BGZF and query it with pybgzf (#52) (8e0299c)

Performance

• Store features in superintervals and short-circuit overlaps (#54) (83d9450)

2.0.0

Breaking

• Make BED records immutable and hashable (#45) (fb194ce)
• Require typeline 2.0 and read and write BED without quoting (#48) (788c172)

Bug Fixes

• Allow zero-length features and check records against the BED spec (#44) (cb7e76b)

Continuous Integration

• Bump the github-actions group with 4 updates (#42) (1726d73)
• Tidy test, lint, and type check settings, and the tests (#49) (db160f9)
• Bump to 2.0.0 (#51) (4279081)

Documentation

• Show reading and writing compressed BED (#50) (8e00834)

Features

• Add BED9 and the ENCODE narrowPeak, broadPeak, and gappedPeak formats (#46) (caa147a)
• Find overlaps on the same strand only (#47) (648c135)