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chore: fixup docs slightly
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clintval committed Aug 2, 2024
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11 changes: 5 additions & 6 deletions pybedlite/overlap_detector.py
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Utility Classes for Querying Overlaps with Genomic Regions
----------------------------------------------------------
The :class:`~pybedlite.overlap_detector.OverlapDetector` class detects and returns overlaps between
a set of regions and another region on a reference. The overlap detector may contain any
interval-like Python objects that have the following properties:
a set of regions and another region on a reference. The overlap detector may contain a collection
of interval-like Python objects that have the following properties:
* `refname` (str): The reference sequence name
* `start` (int): A 0-based start position
* `end` (int): A 0-based exclusive end position
This is encapsulated in the :class:`~pybedlite.overlap_detector.Span` protocol.
This contract is described by the :class:`~pybedlite.overlap_detector.Span` protocol.
Interval-like Python objects may also contain strandedness information which will be used
for sorting them in :func:`~pybedlite.overlap_detector.OverlapDetector.get_overlaps` using
the following property if it is present, otherwise assumed to be positive stranded:
the following property if it is present:
* `negative (bool)`: True if the interval is negatively stranded, False if the interval is
unstranded or positively stranded
This is encapsulated in the :class:`~pybedlite.overlap_detector.StrandedSpan` protocol.
This contract is described by the :class:`~pybedlite.overlap_detector.StrandedSpan` protocol.
Examples of Detecting Overlaps
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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