Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

Support for building a genome graph from multiple MSAs and/or genome sub-graphs built by make_prg. Addresses #130.
CONTRIBUTING.md document

Changed

Dependencies: added make_prg and pybedtools, updated biopython version.

1.9.0 - 25/01/2022

Added

This Changelog
Static executable statically-linked against glibc/libgcc/libstd++ [#101,#163]
Script to build the gramtools backend (build.sh). Simplifies CI (docker image building), removes hacking into setup.py, and simplifies compiling on user machine.

Changed

Switched from setup.py to pyproject.toml and setup.cfg [#164], following PEP517

Removed

Retired variant-aware kmer indexing code [#159]
No longer install py-cortex-api by default. If gramtools discover is used, its installation is requested

Fixed

Variant rebasing in discover was incompletely tested- simplified algorithm and added tests
Infinite loop when no reads mapped to genome graph

1.8.0 - 18/05/2021

Added

Use conan dependency manager for available dependencies (boost, gtest, json) [#158]
Region-based (chr:start-stop) subgraph visualisation (libgramtools/submods/visualise_prg)

Changed

Bump CMake requirements to 3.1.2
Bump boost libraries to 1.69.0