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Latest Version
Avg Release Cycle
313 days
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Changelog History

  • v1.0.4 Changes

    🚀 This is a release with some major changes.

    Important changes:

    • vcfwave is introduced and vcfallelicprimitimes is now considered obsolete
    • 📜 INFO fields output order is now the same as on input parsing

    TODO

    • 🔀 [ ] 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)

  • v1.0.3 Changes

    🚀 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 shell instead of guix environment for development
    • 📄 Regenerated online docs
    • 🚚 README: add matrix badge (removed gitter badge)

  • v1.0.2 Changes

    🚀 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 Changes

    September 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 Changes

    September 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 Changes

    August 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 #!/usr/bin/env python3 hashbangs.

    🏗 ⚠️ Please use git clone --recursive when building this package because it uses sub-modules
    which are not included the source tarballs below.

  • v1.0.0-rc2

    August 15, 2018

  • v1.0.0-rc1 Changes

    February 08, 2016

    Resolves #131

  • v1.0.0-rc0

    June 16, 2015