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@adamnovak adamnovak released this 30 Mar 17:57
· 5272 commits to master since this release
v1.23.0
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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:v1.23.0

Buildable Source Tarball: vg-v1.23.0.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:

  • vg construct now rejects not-yet-implemented * allele from new VCF spec
  • vg CI now runs on Kubernetes
  • vg Docker can now be built with Kaniko
  • vg gaffe now has MAPQ capping logic to reduce the error rate at MAPQ 60
  • Default MAPQ settings in vg mpmap have been changed
  • vg CI tests now respect the core limit of the container they are running in, instead of trying to use all the host's cores
  • A variety of vg mpmap options were removed. Some short options changed their meanings.
  • Mapping real RNA data with vg mpmap is now faster
  • vg CI tests now use an updated toil-vg
  • vg circularize adds graph edges once again when circularizing paths
  • vg gaffe is now faster
  • vg mpmap MAPQs are no longer miscomputed in rare cases
  • vg gaffe's index finding has been completely redone. It can now create its own indexes or find indexes by prefix. This may lead to it picking up and using indexes that were not passed to it directly.
  • Surjection of softclips has been improved.
  • vg call now uses a better, flow-based traversal finding algorithm to generate alleles
  • vg mpmap uses new algorithms for long-read alignment
  • vg CI reports are no longer totally empty for some tests
  • The internal XdropAligner is now much simpler
  • ProtoHandleGraph is no longer needed and has been removed
  • vg concat now works via the HandleGraph API, and has a -p option be path-guided
  • HashGraph no longer crashes when incrementing node IDs
  • Machinery for haplotype-based rescue in vg gaffe has been added
  • XdropAligner now automatically finds the best pinning location

New and Updated Submodules

The gbwtgraph and libbdsg submodules have been updated.

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

Assets 4
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