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)