Vcflib v1.0.4 Release Notes
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🚀 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)