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vg 1.68.0 - Rimbocchi

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@adamnovak adamnovak released this 25 Aug 20:34
· 4 commits to master since this release
v1.68.0
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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:v1.68.0

Buildable Source Tarball: vg-v1.68.0.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 index now accepts a -w option to up-weight nodes to push the top-level chain through them when finding snarls
  • Added a warning that path selection options are not compatible with vg paths -g
  • vg haplotypes exits with an error if the snarl decomposition contains a cyclical top-level chain.
  • scripts/check_options.py now catches if something other than , is between shortform and longform options
  • Add option vg autoindex --no-guessing to allow force-regenerating indices
  • Lookup of regions within paths that are themselves subpaths (like Stella_v1p1#0#Chr4__Stella_v1p1[11578420-11580540]:0-100) should now work again.
  • Add errors when using incompatible options in vg depth
  • SAM-style tags are no longer lost on unmapped reads during surject
  • vg's vcflib build will now use the default python3 instead of the latest installed Python (which might not have its headers)
  • Add nodes as a vg filter --tsv-out field option; prints a comma-separated list of nodes traversed by the read's path
  • vg giraffe now has a --softclip-penalty flag to reduce alignment scores per-base for softclips
  • vg filter now has a -W/--overwite-score flag to save the scores from --rescore.
  • vg filter now checks to make sure you aren't using --rescore or related options when they would do nothing.
  • Internal changes in vg giraffe to allow multiple presets to potentially share settings.
  • Bug fixes for chain transition distance measurement with the zip code tree in vg giraffe
  • vg now supports Protobuf 30+ and its string view return types.
  • vg mod now has an --invert-keep-paths option to save the complement of path names passed to --keep-paths
  • vg giraffe -b hifi preset now uses a --max-min-chain-score of 100
  • vg now has a libbdsg that can run is_regular_snarl() on a distance-less distance index.

Updated Submodules

  • gbwtgraph
  • libbdsg
  • libvgio
Assets 5
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