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vg v1.47.0 - Ostuni
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@adamnovak adamnovak released this 27 Mar 18:51
· 2210 commits to master since this release
v1.47.0
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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:v1.47.0

Buildable Source Tarball: vg-v1.47.0.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 sim and vg stats -a sped up for GBZ input
  • Giraffe now uses the watchdog to detect slow reads
  • vg construct should no longer fail assertions and will instead report errors.
  • vg construct now handles IUPAC codes in the reference as Ns even if they are covered by symbolic structural variants
  • Faster haplotype sampling with vg haplotypes.
  • vg stats -a also outputs statistics on alignment scores and mapping quality.
  • vg giraffe should no longer crash if the distance index is read-only.
  • vg rna now supports the GBZ format for the input graph and haplotypes (new option --gbz-format).
  • vg convert now defaults to PackedGraph instead of HashGraph if no output format selected.
  • New option vg clip -s to remove stubs (dangling nodes not on ref path)
  • vg call and vg deconstruct now only apply node ID translation from GBZ inputs if new -O is used.
  • vg surject will now enforce that the reads it is surjection actually were mapped against the graph you are surjecting against. Right now it checks node IDs and lengths. You can turn this off with -V/--no-validate.
  • vg gbwt now accepts a -I/--gg-in option, which lets you load a .gg file and a .gbwt file and combine them into a .gbz graph.
  • vg validate now accepts a -A/--gam-only option which will validate only the provided alignment's agreement with the graph, and not the graph itself.
  • The vg surject/vg giraffe error: couldn't identify a path corresponding to surjected read error message has been improved to dump more information about the offending read and path.
  • When selecting paths to surject to, a warning will now be printed if the user asks for a path with a []-enclosed subrange at the end. The base path name without the [] subrange coordinates should usually be used instead, because that is the space in which the SAM/BAM output will have its coordinates specified.
  • The vg surject Graph does not have a path named error message should now no longer print pointer values, and is extended to explain a bit more about subpaths.

Updated Submodules

The kff-cpp-api and libbdsg submodules have been updated.

Assets 4
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