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RELEASE_NOTES.md

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For contributions see contributors and commits.

TODO

  • vcfcreatemulti: fix problem with slow and wrong complex regions (implement backtrack) + [ ] check for indels which are really the same + [ ] combine vcfwave duplicated functionality
  • bgzip
  • tabix -p vcf my_file.vcf.gz
  • pangenie, vg deconstruct, vcfbub

ChangeLog v1.0.11-pre ()

  • Stopped vendoring wfa2lib by default - so now the Debian build command is cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -DZIG=OFF ..

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.

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)

ChangeLog v1.0.5 (20230116)

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.

ChangeLog v1.0.3 (20220122)

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)

ChangeLog v1.0.2 (20210104)

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
  • 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 and man pages for all utilities. Created a script bin2md for markdown generation and use pandoc for the man page generation.

Older changes

For older changes view the git log.