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You might also take a look at this genomics-focused sqlite extension: As described in the repository README: This SQLite3 loadable extension adds features to the ubiquitous embedded RDBMS supporting applications in genome bioinformatics: genomic range indexing for overlap queries & joins in-SQL utility functions, e....


The clodius tool puts tab-delimited data from a BED file into an rtree in a sqlite3 database: Data are stored in this database at multiple "zoom levels", which allows for fast queries at wide genomic extents:

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