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vg 1.30.0 - Carentino
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@adamnovak adamnovak released this 19 Jan 22:01
· 3592 commits to master since this release
v1.30.0
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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:v1.30.0

Buildable Source Tarball: vg-v1.30.0.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 paths now has -C option to list which paths are cyclic and which aren't
  • fixed vg view bug which caused outputting to GFA to use too much memory
  • Giraffe can now --show-work to explain itself.
  • Giraffe funnel plots no longer invent fake candidates
  • Giraffe now maps and caps MAPQs properly with syncmers
  • vg mpmap produces more complete multipath alignments around indels in low complexity sequences.
  • Update libvgio dependency (fixed cmake handlegraph dependency)
  • The following subcommands are now deprecated: combine, compare, explode, join, kmers, locify, msga, recalibrate, sift, sort, srpe, translate.
  • The following subcommands have been deleted: bugs, crash.
  • Crash reports now direct users directly to the new issue URL
  • rocksdb is no longer a dependency.
  • vg index no longer will produce RocksDB indexes of GAMs or graphs.
  • vg find can no longer be used to query from RocksDB indexes.
  • vg genotype no longer accepts RocksDB GAM indexes, and instead accepts only GAMs.
  • vg gamsort can no longer sort using the RocksDB order.
  • vg compare has been removed.
  • vg locify has been removed.
  • The following subcommands are now deprecated: concat, explode, join, kmers, msga, recalibrate, sift, sort, srpe, translate.
  • vg prune is now more memory efficient.
  • Giraffe mapping quality cap is now more numerically stable and fails assertions less
  • The roc plot script now runs

New and Updated Submodules

A submodule for the wiki has been added in doc/wiki.

Thelibbdsg, libhandlegraph, and libvgio submodules have been updated.

The rocksdb submodule has been removed.

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

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