🚀 This is a release with some major changes.
- vcfwave is introduced and vcfallelicprimitimes is now considered obsolete
- 📜 INFO fields output order is now the same as on input parsing
- 🔀 [ ] vcfwave check merging of genotypes - write tests
- 🔀 [ ] vcfwave recompute AC, AFs from merged record
- 🚀 [ ] RELEASE 1.0.4
- 🔀 [ ] vcfcreatemulti merge multiple rows
- [ ] rewrite vcfcreatemulti
- [ ] check for indels which are really the same
- [ ] combine vcfwave duplicated functionality
- 🚀 [ ] RELEASE 1.0.5
- [ ] vcfuniq combine genotypes from non-unique records
- [ ] vcfwave check polyploids
- 🚀 [ ] RELEASE 1.0.6
Introduction of O(n) wavefront algorithm WF to replace O(n2) Smith-Waterman SW. Note that the output is different from the original SW implementation. SW is still optionally available but considered obsolete. Use the bi-directional vcfwave instead of vcfallelicprimitives.
- ➕ Added realignment using the wavefront algorithm (now the default). See [vcfwave](./doc/vcfwave.md) (thank you Erik Garrison https://github.com/ekg and Santiago Marco-Sola https://github.com/smarco).
- 👌 Support longer read inversions in vcfwave!
- vcfallelicprimitives now considered legacy/obsolete
- 👌 Improved CMake configuration
- 👀 vcflib compiles with both gcc and clang++ and tests pass, see [guix-clang.scm](./guix-clang.scm) - mind that git submodules such as WFA2-lib still override to gcc
- 🛠 Fixed local build for tabixpp+htslib - note that htslib should be an upstream released version (currently 1.15.1). Unfortunately git submodule does not handle tags.
- 🛠 Fix for -L switch for vcfallelicprimitives
- ➕ Added libasan and lto support
- ✂ Removed useless googletest submodule
- ➕ Added python bindings with pybind11
- ➕ Added python testing framework
- ➕ Added tabixpp back in as a submodule, fixes https://github.com/vcflib/vcflib/issues/305
- 🛠 Optimizations and bug fixes. (thanks @mphschmitt)
🚀 This is a maintenance release of vcflib.
- 🔀 Merge intervaltree changes (thanks @jnunn and @timmassingham)
- Built with gcc-11
- 🛠 Fix issue #251 hapLrt: fix segfault when accessing genotype field. (thanks @mphschmitt)
- 🛠 Fix vcfflatten: fix segfault when no 'AF' field is present (#47, thanks @mphschmitt)
- 🛠 Fixes on vcfnulldotslashdot #310 (thanks @WinterFor)
- 🛠 Fix issue #301: Replace raw pointer usage with std::unique_ptr #306 (thanks @Glebanister)
- 🛠 Fix man page installation #321 (thanks @alexreg)
- 👉 Use
guix shellinstead of
guix environmentfor development
- 📄 Regenerated online docs
- 🚚 README: add matrix badge (removed gitter badge)
🚀 This is a maintenance release of vcflib, mostly improving the build 👷 system, CI and generating markdown docs as well as man pages.
- ✂ Removed tabixpp and htslib source dependencies, i.e., we are now using the distro provided libraries and include files through pkg-config. See also the [README](README.md#build-from-source)
- ✂ Removed the tabixpp+htslib git submodules
- 👷 Generalise and document the cmake build system
- ➕ Added tests to the cmake build system and build instructions to README
- ➕ Added support for ARM64 and PowerPC, see #292 (thanks @genisysram and @mr-c)
- ➕ Added github actions for the issue tracker
- ➕ Added githum CI
- ⚡️ Updated header files in src with copyright/license info, see #16
- 📄 Created markdown [docs](./doc/vcflib.md) and [man pages](./man/) for all utilities. Created a script bin2md for markdown generation and use pandoc for the man page generation.
v1.0.1 ChangesSeptember 30, 2019
- migrate helper scripts to python3
- 👌 Improved docs
- 🛠 fix typos
- ⚡️ updated makefile
- 🏗 promote use of brew and conda over building locally
v1.0.0 ChangesSeptember 03, 2019
🔀 This synchronizes a number of changes that the vgteam has implemented on top of vcflib, including a new intervaltree implementation. Enjoy!
v1.0.0-rc3 ChangesAugust 23, 2019
🍱 🐍 Some of the
vcf*tools were actually Python 2.x scripts, which is EOL soon.
These are now Python 3.x and use
🏗 ⚠️ Please use
git clone --recursivewhen building this package because it uses sub-modules
which are not included the source tarballs below.
v1.0.0-rc2August 15, 2018
v1.0.0-rc1 ChangesFebruary 08, 2016
v1.0.0-rc0June 16, 2015