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Sync upstream - #28

Merged

adamnovak merged 158 commits into

masterfrom

sync-upstream

Jul 2, 2026

Commits on Jan 6, 2025
- Rework CMake config to use targets
  adamnovak
  committed
  8ba2d79
- Update comment
  adamnovak
  committed
  a6c088f
Commits on Feb 18, 2025
- Use find_path to set WFA_INCLUDE_DIRS
  cho-m
  committed
  9f9237f
Commits on Feb 19, 2025
- Enable shared libraries via `-DBUILD_SHARED_LIBS=ON`
  cho-m
  committed
  6ca0f5f
- Install WFBINS, use standard mandir, add tabix.hpp if needed
  cho-m
  committed
  aeaf9ec
Commits on Mar 28, 2025
- Removed loadIndices duplication
  RedPenguin100
  committed
  f537fb3
Commits on Mar 31, 2025
Commits on Apr 2, 2025
- Add include guards
  RedPenguin100
  committed
  e4ed6f1
- removed <iostream> in .h files where not needed
  RedPenguin100
  committed
  35ea1fe
Commits on Apr 3, 2025
- ranged based for loop in a few places
  RedPenguin100
  committed
  724be2e
- make_unique can be used since C++14
  RedPenguin100
  committed
  2306cd7
- Deal with memory leaks
  RedPenguin100
  committed
  30d6554
- More range-based for loop refactor
  RedPenguin100
  committed
  5814be8
- removed duplicate
  RedPenguin100
  committed
  c8acbf3
Commits on Apr 5, 2025
- modernize-loop-convert
  RedPenguin100
  committed
  32582b5
Commits on Apr 7, 2025
- fixed CI and added more python versions
  RedPenguin100
  committed
  c07828f
- amybe fix 2
  RedPenguin100
  committed
  dc9ba4f
- revert to 22.04
  RedPenguin100
  committed
  458b4d5
- revert
  RedPenguin100
  committed
  ba6893e
- revert for real
  RedPenguin100
  committed
  e6374d9
- maybe fix
  RedPenguin100
  committed
  7d0ad87
- add more tests
  RedPenguin100
  committed
  58ef31f
- understand error
  RedPenguin100
  committed
  5735947
- add missing dependency of ubuntu 24.04
  RedPenguin100
  committed
  ca39e3d
- fixed CI properly
  RedPenguin100
  committed
  7901716
- switch order
  RedPenguin100
  committed
  5484ca5
- space
  RedPenguin100
  committed
  d1ce4c5
- Merge branch 'hotfix/ci_fix' into modernize_and_memory_leak
  RedPenguin100
  committed
  f515c4c
- fix compile issues
  RedPenguin100
  committed
  84e4b61
- more range-based changes
  RedPenguin100
  committed
  cf9e3d0
Commits on Apr 8, 2025
- Merge pull request #420 from RedPenguin100/hotfix/ci_fix
  pjotrp
  authored
  2f82606
- Merge pull request #419 from RedPenguin100/modernize_and_memory_leak
  pjotrp
  authored
  c4c1149
Commits on Apr 11, 2025
- Refactoring to remove loadPhased function duplication. Also moved logic to .cpp file to prevent compilation time from rising.
  RedPenguin100
  committed
  8b1b470
Commits on Apr 12, 2025
- Also remove median/mean duplication, opportunistically moved also variance and standard_deviation to stats.hpp file
  RedPenguin100
  committed
  89ffaca
Commits on Apr 13, 2025
- Fixed issue #409 by adding a more unique identifier the variant does not drop anymore
  RedPenguin100
  committed
  0aef3b2
- Added test for the bugfix
  RedPenguin100
  committed
  da3b39e
- Added opportunitic refactors
  RedPenguin100
  committed
  901cd5a
- fix include issue
  RedPenguin100
  committed
  712e128
- revert accidental commit
  RedPenguin100
  committed
  c47958f
- rearrange testing case
  RedPenguin100
  committed
  5bd6070
- fix regression test
  RedPenguin100
  committed
  9f52255
- add test
  RedPenguin100
  committed
  3b7eeab
- rebase vcfwave_4 regression test per the new fixes
  RedPenguin100
  committed
  f532e4f
- more opportunisic addressing calng-tidy warnings refactor
  RedPenguin100
  committed
  ac26105
Commits on Apr 16, 2025
- Merge pull request #421 from RedPenguin100/feature/duplicate_functions
  pjotrp
  authored
  97e5224
- Merge pull request #422 from RedPenguin100/fix/variant_drop
  pjotrp
  authored
  6d39c60
Commits on Apr 17, 2025
- Conflict in github actions file
  pjotrp
  committed
  aa1b7f2
- Release notes, bump version, add release protocol and more on Zig
  pjotrp
  committed
  9bd9b93
- guix.scm we can use the -F switch
  pjotrp
  committed
  5bae713
- Trying to fix github CI
  pjotrp
  committed
  996be7b
- Updated copyright on doc files
  pjotrp
  committed
  061ab55
- Updating RELEASE NOTES
  pjotrp
  committed
  9e7b0fc
- Reverted making Canonicalize a subclass because of https://github.com/vcflib/vcflib/issues/417
  pjotrp
  committed
  c3e89e4
- Disabling failing test
  pjotrp
  committed
  ba5043c
- Remove canocalize.cpp file from build
  pjotrp
  committed
  df8496a
Commits on Apr 18, 2025
- Release v1.0.13
  pjotrp
  committed
  50c1a70
- Zig build: make sure the cache can be used, also in containers
  pjotrp
  committed
  31f2c2c
- README: released static binaries
  pjotrp
  committed
  f5c8f7e
- Hack for static builds --- need to clean up
  pjotrp
  committed
  fbda9e7
- README: update Guix badge
  pjotrp
  committed
  9dfe90c
- guix: preparing for a working full build
  pjotrp
  committed
  f01c61b
- Build system: some cleanup
  pjotrp
  committed
  00033e7
Commits on Apr 19, 2025
Commits on Apr 20, 2025
- Added more const / const ref in places where it was possible
  RedPenguin100
  committed
  303a6ec
- Try to fix badge
  pjotrp
  committed
  fe3f209
- guix build: fixed pyvcflib test
  pjotrp
  committed
  1d84455
- Some build cleanup
  pjotrp
  committed
  e9d01fa
Commits on Apr 21, 2025
- Update RELEASE NOTES
  pjotrp
  committed
  bc9529f
- Wrapping up changes
  RedPenguin100
  committed
  1545103
Commits on Apr 26, 2025
Commits on Apr 27, 2025
- Merge pull request #427 from RedPenguin100/clang_tidy_performance
  RedPenguin100
  authored
  95d5402
- Merge pull request #426 from vcflib/fix/zig_0_14_split
  pjotrp
  authored
  37a5403
- Release notes
  pjotrp
  committed
  dc9dbac
- guix: set zig at 0.14
  pjotrp
  committed
  af5c3df
Commits on May 2, 2025
- Include refactor, and addressing some opportunistic comments from clang-tidy, including
  RedPenguin100
  committed
  cc07843
- Fix TABIXPP_LOCAL --> tabixpp_LOCAL
  RedPenguin100
  committed
  05e6f53
- Fix mistake added in previous PR
  RedPenguin100
  committed
  a595054
- More minor fixes
  RedPenguin100
  committed
  27024ce
Commits on May 3, 2025
- More minor fixes, add TODO on potential bug
  RedPenguin100
  committed
  8361b79
Commits on May 7, 2025
- Merge pull request #429 from vcflib/refactor/organizing_project
  pjotrp
  authored
  6132d0c
- Merge pull request #430 from vcflib/fix/cmake_variable
  pjotrp
  authored
  cb25dfa
Commits on May 17, 2025
- cmake: fix building static/shared libraries
  pjotrp
  committed
  288cb6e
- RELEASE NOTES
  pjotrp
  committed
  4343a20
- README
  pjotrp
  committed
  be13599
Commits on May 18, 2025
- Update docs
  pjotrp
  committed
  9e8c019
- README
  pjotrp
  committed
  6404b90
Commits on Jun 26, 2025
- Fix iterator usage in vcfkeepinfo
  jkmatila
  committed
  aa8e95e
Commits on Jun 27, 2025
- Merge pull request #432 from Euformatics/fix-vcfkeepinfo-iterator
  pjotrp
  authored
  ad56090
Commits on Jul 5, 2025
- Fix iterator usage in vcfremoveaberrantgenotypes
  jkmatila
  committed
  c094934
Commits on Jul 6, 2025
- Merge pull request #434 from Euformatics/fix-vcfremoveaberrantgenotypes-iterator
  pjotrp
  authored
  885afe1
Commits on Oct 28, 2025
- minor fixes
  glennhickey
  committed
  922d8dc
- fix del range check off-by-one
  glennhickey
  committed
  fc720dd
Commits on Oct 29, 2025
- Merge pull request #436 from glennhickey/vcwave-bug
  pjotrp
  authored
  3d63c20
- update vcfwave regression data
  glennhickey
  committed
  669857c
Commits on Oct 31, 2025
- Merge pull request #437 from glennhickey/vcwave-bug
  pjotrp
  authored
  8b5d4c8
Commits on Mar 17, 2026
- Added include files (Variant.h): these are used by vg [AI]
  pjotrp
  committed
  b7590db
- add(pkgconfig): add support for pkgconfig
  pjotrp
  committed
  478f35e
Commits on Mar 18, 2026
- Fix iterator usage in vcfkeepinfo
  
  jkmatila
  authored and
  pjotrp
  committed
  827f2ca
- Fix iterator usage in vcfremoveaberrantgenotypes
  
  jkmatila
  authored and
  pjotrp
  committed
  427779b
- minor fixes
  
  glennhickey
  authored and
  pjotrp
  committed
  33c5253
- fix del range check off-by-one
  
  glennhickey
  authored and
  pjotrp
  committed
  3138067
- update vcfwave regression data
  
  glennhickey
  authored and
  pjotrp
  committed
  8e16e1f
- Added include files (Variant.h): these are used by vg [AI]
  pjotrp
  committed
  aadbba3
- add(pkgconfig): add support for pkgconfig
  pjotrp
  committed
  3c252bb
- Preparing for release
  pjotrp
  committed
  8ef3ea3
- fix build (guix.scm) by using wfa2-lib/fixed
  pjotrp
  committed
  13ca122
- update (guix.scm) zig to latest stable version on guix
  pjotrp
  committed
  49d2db8
Commits on Mar 19, 2026
- Fix static build (CMake) by adding zig flags [AI]
  pjotrp
  committed
  642eda4
- Update (guix.scm) use local wfa2-lib package until it is updated upstream
  pjotrp
  committed
  51ed9ab
- Removed guix badge (README) as it is no longer in Guix upstream. Note the included guix.scm builds static binaries fine, including zig
  pjotrp
  committed
  7b49475
- Update (docs) regenerate for release and bumped version to 1.0.15
  pjotrp
  committed
  95a6c96
- update(github CI)
  pjotrp
  committed
  4b22953
- update(github CI)
  pjotrp
  committed
  a29d1c2
- update(github CI)
  pjotrp
  committed
  0e341a1
- fix zig (vcfcreatemulti) to support later versions
  pjotrp
  committed
  30c7bbd
- Updated (vcfcreatemulti) using zig 0.15 or later
  pjotrp
  committed
  dfd84cf
- RELEASE NOTES
  pjotrp
  committed
  dd768c5
- Merge pull request #442 from pjotrp/pjotrp-master
  pjotrp
  authored
  dc9de89
Commits on Mar 20, 2026
- comment (guix.scm) on supporting zig
  pjotrp
  committed
  ec74dce
- Merge branch 'pjotrp-master'
  pjotrp
  committed
  2ac7999
- Update submodules
  pjotrp
  committed
  3d7e6c5
- comment (guix.scm) on supporting zig
  pjotrp
  committed
  c6b085e
- Update submodules
  pjotrp
  committed
  1119548
- Fix build (guix.scm) vcflib-local-htslib-git - i.e., using git submodules only [AI]
  pjotrp
  committed
  0771a75
- Use gexp (guix.scm) slight improvement
  pjotrp
  committed
  64c4214
- Merge branch 'pjotrp-master'
  pjotrp
  committed
  8911cb2
- gitignore zig output
  pjotrp
  committed
  5679120
- Tests pass (guix.scm) for the static build
  pjotrp
  committed
  1c96c55
- Added (TODO.md) with comment on Debian packaging
  pjotrp
  committed
  29d35c0
- Comment (TODO.md) for Debian packagers
  pjotrp
  committed
  beef669
- Container - add command to create singularity container
  pjotrp
  committed
  60bcb80
- Add (Docker) support
  pjotrp
  committed
  0d40ff1
- md5sums added (RELEASE NOTES)
  pjotrp
  committed
  74bfa6c
- Update (README) with info on singularity, docker and zig
  pjotrp
  committed
  b0d5e3d
- Add note (guix) this file is out of date
  pjotrp
  committed
  e995442
- Fix build (guix.scm) vcflib-local-htslib-git - i.e., using git submodules only [AI]
  pjotrp
  committed
  cf1f16f
- Use gexp (guix.scm) slight improvement
  pjotrp
  committed
  f9b78b9
- Merge branch 'pjotrp-master'
  pjotrp
  committed
  70d0d0a
- Use gexp (guix.scm) slight improvement
  pjotrp
  committed
  2596ee1
- Fix build (guix.scm) vcflib-local-htslib-git - i.e., using git submodules only [AI]
  pjotrp
  committed
  b118a9b
Commits on Jun 30, 2026
- Reapply "Duplicate name handling"
  adamnovak
  committed
  6ffda65
- Merge branch 'update-fastahack-only' into sync-upstream
  adamnovak
  committed
  38e5171
- Merge remote-tracking branch 'origin/master' into sync-upstream
  adamnovak
  committed
  ea48e68
- Make binaries static only individually
  adamnovak
  committed
  41e285c
Commits on Jul 1, 2026
- Merge branch 'update-fastahack-only' into HEAD
  adamnovak
  committed
  174bcf5
Commits on Jul 2, 2026
- Merge remote-tracking branch 'vgteam/master' into sync-upstream
  adamnovak
  committed
  6439438

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Commits on Mar 18, 2026