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@adamnovak adamnovak released this 16 Aug 20:32
· 2916 commits to master since this release
v1.34.0
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Learn about vigilant mode.

Download for Linux

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.34.0

Buildable Source Tarball: vg-v1.34.0.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:

  • Support for the GBZ format (GBWT + GBWTGraph):
    • vg autoindex: --workflow giraffe outputs GBZ instead of GBWT and GBWTGraph.
    • vg convert: GBZ -> other graph types.
    • vg gbwt: GBWT + GBWTGraph <-> GBZ.
    • vg giraffe: GBZ as the default input format for GBWT + GBWTGraph.
    • vg index: Graph format for distance index construction.
    • vg minimizer: An alternative to GBWT + graph.
    • vg snarls: Graph format with options that do not need embedded paths.
  • vg convert outputs HashGraph instead of VG by default.
  • GBWT / GBWTGraph / GCSA2 structures are serialized as bare files for better compatibility with external tools.
  • vg convert -w can now handle separator tokens in contig names
  • Docker base images are now pulled through Google's cache
  • vg giraffe now uses IndexRegistry instead of IndexManager and demands that passed file names already exist
  • Wiki now includes a tutorial under test for Giraffe
  • vg benchmark evaluates the minimum distance index
  • Improved build out of the box on M1 Macs with Homebrew
  • vg deconstruct now writes "Allele Traversals" (AT field in INFO) for each site. The traversals map the alleles to paths in the graph.
  • IntegratedSnarlFinder properly generates single-node chains for bridge edges in the Cactus graph.
  • Allow seeding path traversals from XG path set even when we are using GBWT input for vg deconstruct.
  • vg index, vg minimizer, and vg snarls can load GBZ without a distinguishing option
  • vg mpmap now uses the RNA mapping preset (--nt-type rna) by default instead of DNA (--nt-type dna)
  • Fixed a bug that sometimes caused incomplete multipath alignments from vg mpmap
  • IntegratedSnarlFinder properly tracks whether cycles and bridge edge paths have been reached regardless of orientation
  • Minimizer indexes no longer incorrectly cache distances for looping chains, fixing a duplicate-alignment, low-MAPQ bug in Giraffe
  • DYNAMIC now has hopscotch-map as a sub-submodule
  • vg autoindex can create GBZ files for vg giraffe using a GFA with W-lines as input
  • The speed of vg mpmap is more robust to low-quality RNA-seq reads
  • Multipath alignments can be viewed in dot format with vg view -Kd
  • vg clip added to remove alt alleles in bed regions or low-path-depth alleles from the graph

New and Updated Submodules

DYNAMIC, gbwt, gbwtgraph, libvgio, libbdsg, gssw, and sdsl-lite have been updated.

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

Assets 4
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