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vg 1.36.0 - Cibottola
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@StephenHwang StephenHwang released this 08 Nov 22:30
· 2589 commits to master since this release
v1.36.0
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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:v1.36.0

Buildable Source Tarball: vg-v1.36.0.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:

  • Builds again on Ubuntu 18.04
  • Giraffe records read and pair mapping wall clock times
  • Giraffe can no longer output fragment length annotations too large to convert from JSON to GAM
  • Giraffe no longer uses duplicate minimizers as often for seeds, potentially increasing mapping speed.
  • Giraffe --track-provenance will no longer crash when considering improperly paired mappings
  • Surjection can now prune back low-complexity or short anchors to give more-optimal alignments against the target paths (--prune-low-cplx)
  • GFA file input is now checked by the parser and not just trusted to match the spec
  • Mac CI Homebrew package installation is more robust
  • Better handling of reversing reference paths in vg call
  • Multiple -P allowed in vg clip
  • vg paths messaging cleaned up to acknowledge that vg paths -E -g does indeed need a graph.
  • vg giraffe and vg mpmap no longer crash when reads are in lowercase
  • vg map -h should now print help again
  • CI now supports secure Docker Hub mirrors
  • vg call joins deconstruct and surject in transparently supporting reference subpaths
  • vg deconstruct changed to write LV and PS tags wrt sites in the VCF (and will not longer reference un-exported sites from the graph)
  • vg clip gets -D option for clipping out big deletion edges
  • Specified --align-out parameter in vg sim as GAM-format output
  • PATH is now quoted when added to

New and Updated Submodules

  • gfakluge has been updated.

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

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