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CHANGELOG.md

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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.

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