diff --git a/CHANGELOG.md b/CHANGELOG.md index 922bc682..2ed7c000 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,6 @@ +Changelog +========= -# Changelog All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), @@ -9,6 +10,35 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 [standard-readme]: https://github.com/RichardLitt/standard-readme +## [2.0.0] - 2021-06-21 +### Added +- list of all commandline options +- example for a greedy DENTIST configuration +- guide on how to release a new version of DENTIST (work in progress) + +### Changed +- release v1.0.1 contained breaking changes so this release updates to v2.0.0: + the changes to the workflow make it incompatible with old configuration files +- moved Docker image to Ubuntu and reduced size +- improved compatibility of pre-compiled binaries by compiling on Ubuntu 16.04 +- sort read IDs in `insertions.db` to make AGP and BED files comparable +- allow `--min-*-coverage` in `dentist mask-repetitive-regions` to be zero +- avoid confusing message about pre-fetching the Singularity image if possible +- updated README + +### Removed +- unused argument for `process-pile-ups` +- replaced `Dockerfile.build-release` by regular `Dockerfile` + +### Fixed +- fixed `ProtectedOutputException` bug that was listed in the Troubleshooting + section of the README +- sort LAS files for daccord without chaining +- buffer overflow in `propagate-mask` +- adjust `read-coverage` in example configuration to actual coverage in the + example dataset + + ## [1.0.2] - 2021-04-26 ### Added - provide pre-built binaries of DENTIST and all dependencies in release tarball @@ -18,7 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Improved README a lot - Updated dependencies -- Removed `LAcheck` from the workflow beacuse it is useless +- Removed `LAcheck` from the workflow because it is useless (see [issue 14](https://github.com/a-ludi/dentist/issues/14)) ### Fixed