Genomicsqlite

* New **JDBC driver** supporting any JVM language
* JAR attached, also available via Maven (see [Guide](https://mlin.github.io/GenomicSQLite/))
* [Colab notebook](https://colab.research.google.com/drive/1OlHPOcRQBhDmEnS1wtOdtUGDkcD7LtKx?usp=sharing) updated to demonstrate accessing compressed database via Spark SQL
* A small **format change** makes compressed databases created with previous versions **read-only**
* If needed, the "vacuum into" procedure can restore read/write capability
* No further format changes are planned at this time

[](https://mlin.github.io/GenomicSQLite/) [](https://pypi.org/project/genomicsqlite/) [](https://anaconda.org/mlin/genomicsqlite)

The managed packages bundle these compiled library files, also available for download here to use with C/C++ or other languages:

* **libgenomicsqlite.so** for Linux x86-64 (Haswell), built in Ubuntu 16.04
* **libgenomicsqlite.dylib** for macOS Catalina

An up-to-date version of SQLite itself is also required, as detailed in the [docs](https://mlin.github.io/GenomicSQLite/). Please [file an issue](https://github.com/mlin/GenomicSQLite/issues/new/choose) for any compatibility problems with systems that aren't older than specified above.

**USE AT YOUR OWN RISK:** The extension makes fundamental changes to the SQLite storage layer. While designed to preserve ACID transaction safety, it's young and unlikely to have zero bugs. This project is not associated with the SQLite developers.

* Improved GRI query API: new in-SQL function `genomic_range_rowids()` replaces the need to paste SQL strings during query preparation
* Helper function `genomic_range_index_levels()` detects optimization bounds; see Programming Guide for details
* The original approach is slightly more efficient, so we'll keep supporting it for advanced use; documentation moved to Internals
* New routine helps with "attaching" a GenomicSQLite database to an existing SQLite connection
* Added advice on using GRI with circular chromosomes to Programming Guide

[](https://mlin.github.io/GenomicSQLite/) [](https://pypi.org/project/genomicsqlite/) [](https://anaconda.org/mlin/genomicsqlite)

The Python packages bundle these compiled library files, also available for download here to use with C/C++ or other languages:

* **libgenomicsqlite.so** for Linux x86-64 (Haswell), built in Ubuntu 16.04
* **libgenomicsqlite.dylib** for macOS Catalina

An up-to-date version of SQLite itself is also required, as detailed in the [docs](https://mlin.github.io/GenomicSQLite/). Please [file an issue](https://github.com/mlin/GenomicSQLite/issues/new/choose) for any compatibility problems with systems that aren't older than specified above.

**USE AT YOUR OWN RISK:** The extension makes fundamental changes to the SQLite storage layer. While designed to preserve ACID transaction safety, it's young and unlikely to have zero bugs. This project is not associated with the SQLite developers.

* Improves query speed (workload-dependent) by prefetching & decompressing data on background threads during sequential scans.
* Adds related [tuning options](https://mlin.github.io/GenomicSQLite/guide/#tuning-options)

* fixes C API `genomicsqlite_open()`
* add macOS build to CI and packages

Genesis version

[](https://pypi.org/project/genomicsqlite/) [](https://anaconda.org/mlin/genomicsqlite)

The Python packages bundle these compiled library files, which you may also download separately for use with other languages:

* **libgenomicsqlite.so** for Linux x86-64 (Haswell), built in Ubuntu 16.04

Please [file an issue](https://github.com/mlin/GenomicSQLite/issues/new/choose) for any compatibility issues with OS & CPU that don't appear to be too old based on the above.

**USE AT YOUR OWN RISK:** The extension makes fundamental changes to the SQLite storage layer. While designed to preserve ACID transaction safety, it's young and unlikely to have zero bugs. This project is not associated with the SQLite developers.