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@adamnovak adamnovak released this 20 May 19:02
· 8785 commits to master since this release
v1.16.0
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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:v1.16.0

Buildable Source Tarball: vg-v1.16.0.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:

  • Improvements to the snarl-based clusterer
  • Support for thread names stored in the GBWT, and removal of xg thread name storage
  • Removal of gPBWT construction from vg index
  • GBWT maniputaltion tools in vg gbwt
  • VCF-based snarl traversal finding, for re-calling VCF variants
  • Recall option for vg call
  • GaplessExtension support in the GaplessExtender and in vg gaffe
  • Restored support for loading empty files, most obvious when working with snarls files
  • "Funnel" statistics in vg gaffe
  • Additional vg gaffe heuristics
  • A graph equivalence check algorithm
  • A random handle graph construction algorithm
  • Bugfixes for PackedGraph
  • Serialization support in PackedGraph and HashGraph
  • Improved GBWT thread name syntax
  • Disjoint splice graph support and other improvements in vg rna
  • An updated internal handle graph interface with circular path support, path editing, serialization, and subsequence access
  • Refactoring of IO functionality to go through the new libvgio.
  • Removal of vg.proto, now provided by libvgio.
  • Ability to trim softclips/tips when embedding paths into the graph
  • Distance index improvements
  • properly defined numerical class constants to fix unoptimized builds
  • Giraffe Facts script for evaluating vg gaffe performance
  • Snarl depth in SnarlManager
  • Multiple GAM support in vg chunk
  • Hash-based minimizer index
  • Activation of compiler optimization in libstructures
  • Bugfixes for vg call -f
  • Bugfixes for vg snarls -m
  • Fix for a crash caused by inconsistent handling of Ns.
  • Single-orientation minimizers
  • Fixed multipath alignment validation with self loops
  • Xdrop aligner refactoring and documentation
  • Xdrop support in vg gaffe
  • Permit empty GBWT in vg paths, with a warning
  • Building the maximum distance index is now optional
  • Case-insensitive variant ids
  • Improved PackedGraph storage backend with greater compression
  • Bugfixes to and visualizations for MEMChainModel
  • Bugfixes to chunked alignment
  • Long read mapping preset in vg map
  • Bugfixes to vg construct SV handling and alt path generation
  • Bugfixes to Eades Algorithm sort

New System Dependencies

None

New and Updated Submodules

The libvgio submodule has been added.

The gbwt, gcsa2, libhandlegraph, protobuf, sonLib, structures, and vcflib submodules have been updated.

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

Assets 4
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