ChangeLog v1.0.14 (20250518)

• CMake: Fixed building static libs and shared libs (the previous version just compiled a static lib)
• Updated zig compile for 0.14 (MichaelK)
• Lots of refactoring (MichaelK)
• CMake: Improved linker speeds by moving some libs
• CMake: Improved markdown/pydoc tests, so we don't show the path to the binary
• guix.scm has multiple outputs including static binaries and a test mode
• guix.scm has procedure for building with local htslib and tabixpp only
• Added @RedPenguin100 Michael Kovaliov as a maintainer (welcome!)

Static binaries are available with the previous release.

ChangeLog v1.0.13 (20250417)

• Zig support was added to Guix and Conda - and we expect it to be more common soon
• Addind release protocol to README - so I don't forget bumping version etc.
• Fixed vcfwave issues (see #416) and conda build (thanks Michael Kovaliov, aka @RedPenguin100)
• Fixed github actions (Michael)
• Lots of minor refactoring and cleanup, as well as a memory leak (Michael)
• tabix.hpp fixed and set WFA_INCLUDE_DIRS and -DBUILD_SHARED_LIBS=ON (thanks Michael Cho, aka @cho-m)
• Cmake fixes (thanks Adam Novak)
• Updated simde submodule
• Fix CMakeLists.txt not to try to install wfa-lib when it is a package
• Reverted on Canocalize extraction in Variant class because of downstream use, see #417

Static binaries with man pages can be downloaded (129Mb):

https://files.genenetwork.org/software/vcflib/v9nqzmiln35qk8xraiyzk1hy9sw3mh7y-vcflib-static-git-v1.0.13-0-g50c1a70.tar.gz

md5sum of tarball is 740e20a906c56dc5d37440cdbbc86e7f

ChangeLog v1.0.12 (20241122)

• Improved parsing of INFO and FORMAT lines by @jeizenga in #374
• Support external tabixpp by @adamnovak in #375
• Fix vcfwave.cpp by @AndreaGuarracino in #407
• Use regex to find the '..' between postions and replace it with '-' by @debbyku in #405
• Fix tag-fail long option that was overriden by tag-pass in vcffilter.cpp by @Gullumluvl in #404
• vcfwave: fix condition to avoid nullifying valid SNPs and MNPs by @AndreaGuarracino in #408
• Upgraded Zig support to 0.13.0 by @pjotrp
• Merged multichoose code into vcflib since no one else uses it
• Added sources for canonicalize too
• Moved Fasta.h (fastahack) dependencies from Variant.h into sources
• Updated multichoose and simde modules
• Improved vcfwave support

New Contributors

• @jeizenga made their first contribution in #374
• @debbyku made their first contribution in #405
• @Gullumluvl made their first contribution in #404

Full Changelog: v1.0.10...v1.0.12

ChangeLog v1.0.10 (20240420)

Vcflib maintenance release

• Fixed vcfwave bugs - thanks Andrea Guarracino!
• Fixed c++17 compatability - thanks Alex Petty!
• Fixed tabixpp script - thanks Blaise Li!
• Improved for vcfwave the wfa2lib build, fixed running tests with upstream build update
• Removed deprecated binary_function
• Removed unused files from repo
• Updated README

ChangeLog v1.0.9 (20230211)

Vcflib maintenance release - mostly for including in Debian

• Another fix so downstream packages, such as freebayes, no longer need WFAlib.

Another maintenance release for distros

ChangeLog v1.0.8 (20230210)

Vcflib maintenance release - mostly for including in Debian

• Another fix so downstream packages, such as freebayes, no longer need WFAlib.

ChangeLog v1.0.7 (20230207)

Vcflib maintenance release - mostly for including in Debian

• Fixed regression discovered by garguantua_kerr and atille of Debian (thanks!)
• Added note on bio-vcf in vcffilter doc
• notes on vcfcreatemulti and backtracking
• CMake: honour include(GNUInstallDirs) paths (I forgot)

ChangeLog v1.0.6 (20230129)

Vcflib maintenance release - mostly for including in Debian

• Fixed zig complaining about leaking memory
• Added CMake Debian support with -DWFA_GITMODULE=OFF
• Introduced CMake include(GNUInstallDirs)
• Successfully built wfa2 using embedded CMakeLists.txt
• Cleaned up CMakeLists.txt removing comments etc.
• Reintroduced vcfcreatemulti in legacy mode when ZIG=OFF (for Debian)

Vcflib's first Humpty Dumpty release: vcfcreatemulti is the natural companion to vcfwave.

Often variant callers are not perfect.

vcfwave with its companion tool vcfcreatemulti can take an existing VCF file that contains multiple complex overlapping and even nested alleles and, unlike Humpty Dumpty, take them apart and put them together again.
Thereby, hopefully, creating sane VCF output that is useful for analysis and getting rid of false positives.

We created these tools by including the state-of-the-art biWFA wavefront aligner.
The tools are particularly useful for the output from structural variation callers and pangenome genotypers, such as used by the Human Pangenome Reference Consortium (HPRC) because of overlapping ALT segments.

Important changes:

• vcfwave is introduced and vcfallelicprimitimes is now considered obsolete
• INFO fields output order is now the same with every tool as on input parsing
• vcfwave check merging of genotypes - write tests
• vcfwave recompute AC, AFs from merged record
• Added python bindings with pybind11
• introduced the zig compiler with vcfcreatemulti.cpp as a first target (use cmake ZIG=OFF to disable). At this point the zig version (-n switch) gives identical results.

Introduction of O(n) wavefront algorithm WF to replace O(n^2) 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 (thank you Erik Garrison https://github.com/ekg and Santiago Marco-Sola https://github.com/smarco).
• WFA2-lib fix is merged upstream. Fixes bleeding in of macros #359
• Support longer read inversions in vcfwave!
• vcfallelicprimitives now considered legacy/obsolete
• Fixed allowing for different field order - see #365
• Improved CMake configuration
• vcflib compiles with both gcc and clang++ and tests pass, see 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
• Moved git submodules into ./contrib
• Added python testing framework
• Added tabixpp back in as a submodule, fixes #305
• Optimizations and bug fixes. (thanks @mphschmitt)
• vcfcreatemulti merge multiple rows
• rewrite of vcfcreatemulti using zig
• vcfcreatemulti merge genotypes correctly, with tests
• vcfcreatemulti adjust info and genotypes for variants that have multiple alts already (now errors)
• vcfcreatemulti handle phase
• vcfcreatemulti document building with zig
• vcfcreatemulti added progress bar to vcfwave and vcfcreatemulti with update to tabixpp
• vcfcreatemulti default vcfwave and vcfcreatemulti to nextgen mode
• vcfcreatemulti check file is sorted for vcfcreatemulti and improve suggestions

ChangeLog v1.0.4

Never properly released. Merged with v1.0.5.