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vg 1.74.0 - Petrie

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@adamnovak adamnovak released this 04 May 19:56
· 218 commits to master since this release
v1.74.0
a2bc507

Download for Linux

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.74.0

Buildable Source Tarball: vg-v1.74.0.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:

  • Added vg giraffe --haplotype-sampling to automatically count kmers and haplotype-index and haplotype-sample the graph. Make sure to have kmc installed. Providing either a --kff-name or --haplotype-name will now also trigger generation of the other. To do one-reference sampling, continue to use --set-reference. To do non-diploid sampling with a certain number of haplotypes, use --no-diploid-sampling and --num-haplotypes.
  • vg giraffe will no longer claim to be guessing a GBZ file you definitely told it to use
  • vg paths -u fixed to use use reference path to help root the integrated snarl finder.
  • vg gbwt option --gbz-v1 for writing GBZ version 1 for compatibility with older tools
  • Remove broken vg paths --extract-vg option which would extract a partial Protobuf graph file in a way so poorly explained as to be unusable.
  • Giraffe no longer ignores the parts of seeds that extend outside their graph nodes to the left when scoring them. Note that this can reduce R10 read variant calling accuracy versus the previous release of vg. This regression was fixed before release (see below).
  • Giraffe hifi mapping preset has been re-tuned for new seed score distribution.
  • Chain visualizations no longer need to be panned or zoomed to show changes to the traceback.
  • Chain visualizations no longer accumulate more and more transition lines when mousing in and out of a selected node.
  • Giraffe no longer tries to position-index all haplotypes when showing work. If you need all haplotypes position-indexed for debugging chaining against them, use --haplotype-positions.
  • vg autoindex --gfa will error if the filename seems gzipped
  • vg CI data is no longer hosted under a user public_html directory
  • vg autoindex has a -w sampling workflow to make indexes for haplotype sampling
  • Revised Giraffe chain and alignment scoring. Alignments generated from chains are now no longer scored with the affine gap model used for base-level dynamic programming, but instead are scored with a logged-gap-score, variable-mismatch-penalty model borrowed from minimap2.
  • Calling results from nanopore reads are now better than v1.73.0 again.
  • Simplify an internal return value for align_sequence_between().
  • vg giraffe will now stop with an error when the minimizers or zipcodes are older than the distance index they were supposedly generated from.
  • Add compile-time option to check ziptree iterator for missing seed-to-seed transitions
  • augref-related options in vg paths renamed to be gref-related

Updated Submodules

Thegbwtgraph and libvgio submodules have been updated.

Assets 5
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