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All Projects → mlin → Genomicsqlite

mlin / Genomicsqlite

Licence: apache-2.0
Genomics Extension for SQLite

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sqlitebioinformaticsgenomicssqlite3sequencing

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Genomics Extension for SQLite

("GenomicSQLite")

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.g. reverse-complement DNA, parse "chr1:2,345-6,789"
  • automatic streaming storage compression (also available standalone)
  • reading directly from HTTP(S) URLs (also available standalone)
  • pre-tuned settings for "big data"

This October 2020 poster discusses the context and long-run ambitions:

GenomicSQLite Poster

Our Colab notebook demonstrates key features with Python, one of several language bindings.

USE AT YOUR OWN RISK: The extension makes fundamental changes to the database 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.

Installation & Programming Guide

Start Here 👉 full documentation site

We supply the extension prepackaged for Linux x86-64 and macOS Catalina. An up-to-date version of SQLite itself is also required, as specified in the docs.

Programming language support:

  • C/C++
  • Python ≥3.6
  • Java & JVM languages
  • Rust

More to come. (Help wanted; see Language Bindings Guide)

Building from source

build

Most will prefer to install a pre-built shared library (see above). To build from source, see our Actions yml (Ubuntu 20.04) or Dockerfile (CentOS 7) used to build the more-portable releases. Briefly, you'll need:

  • C++11 build system
  • CMake ≥ 3.14
  • Dev packages: SQLite ≥ 3.31.0, Zstandard ≥ 1.3.4, libcurl

And incantations:

cmake -DCMAKE_BUILD_TYPE=Release -B build .
cmake --build build -j 4 --target genomicsqlite

...generating build/libgenomicsqlite.so. To run the test suite, you'll furthermore need:

  • htslib ≥ 1.9, samtools, and tabix
  • pigz
  • Python ≥ 3.6 and packages: pytest pytest-xdist pre-commit black pylint flake8
  • clang-format & cppcheck

to:

pre-commit run --all-files  # formatters+linters
cmake -DCMAKE_BUILD_TYPE=Debug -B build .
cmake --build build -j 4
env -C build ctest -V
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