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@adamnovak adamnovak released this 11 May 20:40
· 4879 commits to master since this release
v1.24.0
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Download for Linux

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.24.0

Buildable Source Tarball: vg-v1.24.0.tar.gz

Includes source for vg and all submodules. Use this instead of Github's "Source Code" downloads; those will not build as they do not include code for bundled dependencies that the vg build process needs.

This release includes:

  • Bugfixes in vg mpmap
  • MEM finding heuristic in vg mpmap
  • Pointers to Gimbricate and Seqwish when trying to import a non-blunt GFA
  • A new IntegratedSnarlFinder that can be faster and use less memory, accessible through vg snarls --algorithm integrated
  • Use of dozeu library for vg gaffe rescue
  • Faster default mapping parameters in vg rna
  • Fix for excessive memory use bug in spliced vg surject
  • Fix for an off-by-one error in vg annotate gff parser
  • Fix for getting seed distances from distance index
  • Additional spliced vg surject bugfixes
  • Added option to prespecify topological order for dozeu
  • Top level clustering improvements for vg gaffe
  • vg add can now work with various graph formats as input
  • Made banded alignment traceback not recursive
  • Minor optimizations in vg gaffe
  • Added GBWT traversals option for vg call
  • Shook more bugs out of mpmap presets and alignment
  • Added a GBWT traversal finder
  • Improved Turtle Pangenome Ontology
  • Adjusted FTP URL where CI testing looks for its GIAB test data
  • More use of dozeu in vg mpmap
  • Support for quality-adjusted alignment in dozeu
  • Revised vg mpmap CLI for better usability
  • Added a no clustering option to vg mpmap
  • Registered magic numbers for libbdsg graph types so they can be loaded without VPKG encapsulation
  • Added node qualities to vg pack output format
  • Updated internal dozeu and X-drop alignment interface
  • Added ability to simulate from a specific sample in vg sim
  • Update handle graph API to include node ranks
  • Changed XdropAligner usage to be one per thread.
  • Removed support for reading GFAs with overlaps: please preprocess with Seqwish to squash the overlaps out
  • Cap the number of threads used in the Docker build to a reasonable number for Quay potatoes
  • Automask IUPAC codes to Ns in vg construct, because the internal data model can't use them. If you want them in the graph, make them into variants.
  • Chunk long paths when extracting paths Protobuf with vg paths
  • Bugfixes to the ODGI graph implementation
  • Boosted timeout for simulated chr21 CI mapping test
  • Tweaked error rates used for vg call
  • Substantial bugfixes in the FlowCaller
  • Prohibit empty nodes in xg graphs
  • Support for ODGI format in vg convert and as an input format more generally
  • Added libbdsg, xg, and vg's algorithms and io namespaces to vg Doxygen docs
  • Fixed excessive recursion when dealing with snarls
  • Added MAPQ support for paired-end vg gaffe.
  • Added ability to convert GFA files to other graph formats in vg convert

New and Updated Submodules

The dozeu, gbwt, gbwtgraph, gfakluge, gssw, libbdsg, libhandlegraph, pinchesAndCacti, structures, and xg submodules have been updated.

Make sure to git submodule update --init --recursive if building from source.

Assets 4
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