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A Python implementation of the interval binning scheme

Project description

These are some utility functions for working with the interval binning scheme as used in the UCSC Genome Browser. This scheme can be used to implement fast overlap-based querying of intervals, essentially mimicking an R-tree index.

Note that some database systems natively support spatial index methods such as R-trees. See for example the PostGIS extension for PostgreSQL.

Although in principle the method can be used for binning any kind of intervals, be aware that the largest position supported by this implementation is 2^29 (which covers the longest human chromosome).


See the documentation.


To install the latest release via PyPI using pip:

pip install interval-binning

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