vg 1.21.0 - Fanano

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.21.0

Buildable Source Tarball: vg-v1.21.0.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:

• Changes to how vg paths can be used to remove paths from a graph.
• Use of a new toil-vg version in testing.
• Changes to minimizer seed handling algorithms in vg gaffe.
• Some paired-end clustering logic to be used in vg gaffe.
• Improvements to the build system around the libsdsl build.
• No-hit read counting and better S3 support in Giraffe Wrangler script.
• A new subcommand, vg depth.
• Refactoring and race condition removal in vg pack.
• Probabilistic calling support.
• Improvements to snarl traversal enumeration.
• Improved ability of the build system to handle switching compilers.
• Bugfixes to the vg RDF ontology.
• vg augment now cuts off softclips by default.
• vg explode functionality now subsumed by vg chunk.
• Internal VGSet object now supports HandleGraphs.
• Some manpages available via make man.
• Better handling of reverse-strand cycles in vg call.
• Better gtf/gff parsing in vg rna.
• Snarl computation now parallel.
• Subpaths output by vg chunk -p now contain offsets.
• Fix a race condition when reading from the Paths object.
• Ability to chunk non-indexed GAM files by graph component.
• Bugfixes to kmer enumeration.
• Deprecated some vg mod flags, with warning messages.
• vg find can produce more information about kmers.
• vg construct should no longer drop the end breakpoints of deletions.

New and Updated Submodules

The BBHash, libbdsg, libhandlegraph, pinchesAndCacti, and xg submodules have been updated.

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