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Changelog History

  • v1.0.4 Changes

    ๐Ÿš€ This is a release with some major changes.

    Important changes:

    • vcfwave is introduced and vcfallelicprimitimes is now considered obsolete
    • ๐Ÿ“œ INFO fields output order is now the same as on input parsing


    • ๐Ÿ”€ [ ] vcfwave check merging of genotypes - write tests
    • ๐Ÿ”€ [ ] vcfwave recompute AC, AFs from merged record
    • ๐Ÿš€ [ ] RELEASE 1.0.4
    • ๐Ÿ”€ [ ] vcfcreatemulti merge multiple rows
      • [ ] rewrite vcfcreatemulti
      • [ ] check for indels which are really the same
      • [ ] combine vcfwave duplicated functionality
    • ๐Ÿš€ [ ] RELEASE 1.0.5
    • [ ] vcfuniq combine genotypes from non-unique records
    • [ ] vcfwave check polyploids
    • ๐Ÿš€ [ ] 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.

    • โž• Added realignment using the wavefront algorithm (now the default). See [vcfwave](./doc/ (thank you Erik Garrison and Santiago Marco-Sola
    • ๐Ÿ‘Œ Support longer read inversions in vcfwave!
    • vcfallelicprimitives now considered legacy/obsolete
    • ๐Ÿ‘Œ Improved CMake configuration
    • ๐Ÿ‘€ 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
    • ๐Ÿ›  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.
    • ๐Ÿ›  Fix for -L switch for vcfallelicprimitives
    • โž• Added libasan and lto support
    • โœ‚ Removed useless googletest submodule
    • โž• Added python bindings with pybind11
    • โž• Added python testing framework
    • โž• Added tabixpp back in as a submodule, fixes
    • ๐Ÿ›  Optimizations and bug fixes. (thanks @mphschmitt)
  • v1.0.3 Changes

    ๐Ÿš€ This is a maintenance release of vcflib.

    • ๐Ÿ”€ Merge intervaltree changes (thanks @jnunn and @timmassingham)
    • Built with gcc-11
    • ๐Ÿ›  Fix issue #251 hapLrt: fix segfault when accessing genotype field. (thanks @mphschmitt)
    • ๐Ÿ›  Fix vcfflatten: fix segfault when no 'AF' field is present (#47, thanks @mphschmitt)
    • ๐Ÿ›  Fixes on vcfnulldotslashdot #310 (thanks @WinterFor)
    • ๐Ÿ›  Fix issue #301: Replace raw pointer usage with std::unique_ptr #306 (thanks @Glebanister)
    • ๐Ÿ›  Fix man page installation #321 (thanks @alexreg)
    • ๐Ÿ‘‰ Use guix shell instead of guix environment for development
    • ๐Ÿ“„ Regenerated online docs
    • ๐Ÿšš README: add matrix badge (removed gitter badge)
  • v1.0.2 Changes

    ๐Ÿš€ This is a maintenance release of vcflib, mostly improving the build ๐Ÿ‘ท system, CI and generating markdown docs as well as man pages.

    • โœ‚ 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](
    • โœ‚ Removed the tabixpp+htslib git submodules
    • ๐Ÿ‘ท Generalise and document the cmake build system
    • โž• Added tests to the cmake build system and build instructions to README
    • โž• Added support for ARM64 and PowerPC, see #292 (thanks @genisysram and @mr-c)
    • โž• Added github actions for the issue tracker
    • โž• Added githum CI
    • โšก๏ธ Updated header files in src with copyright/license info, see #16
    • ๐Ÿ“„ Created markdown [docs](./doc/ 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
    • ๐Ÿ‘Œ Improved docs
    • ๐Ÿ›  fix typos
    • โšก๏ธ updated makefile
    • ๐Ÿ— promote use of brew and conda over building locally
  • v1.0.0 Changes

    September 03, 2019

    ๐Ÿ”€ 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

    ๐Ÿฑ ๐Ÿ 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.

    ๐Ÿ— โš ๏ธ 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