v0.5.1

• Add SQL functions for parsing genomic range strings like chr1:2,345-6,789
• Fix Rust genomicsqlite_attach_sql() binding

v0.5.0

• Rust bindings, published on crates.io and covered in the docs
• Adds SQL helper functions for storing DNA/RNA sequences as compact BLOBs using two bits per nucleotide.
  • nucleotides_twobit()
  • twobit_dna()
  • twobit_rna()
  • twobit_length()
  • see Programming Guide for details

v0.4.0

• New JDBC driver supporting any JVM language
  • JAR attached, also available via Maven (see Guide)
  • Colab notebook 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

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. Please file an issue 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.

v0.3.0

• 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

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. Please file an issue 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.

v0.2.0

• Improves query speed (workload-dependent) by prefetching & decompressing data on background threads during sequential scans.
• Adds related tuning options

v0.1.5

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

v0.1.3

Genesis version

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 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.