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@adamnovak adamnovak released this 12 Apr 22:36
· 4581 commits to master since this release
v1.32.0
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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:v1.32.0

Buildable Source Tarball: vg-v1.32.0.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:

  • CI now tests with sequenceTubeMap
  • vg map and vg mpmap now annotate properly-paired read mappings
  • vg stats -a reports proper pairing statistics
  • Faster graph to GFA conversion with vg convert.
  • vg surject now gives a helpful warning if you try to use an unsurjectable GAF, rather than just crashing
  • GBWT index can now be used to find alt alleles in vg deconstruct with -g
  • Single nodes at the end of bridge paths in the Cactus graph won't show up twice in the snarl decomposition
  • Giraffe self-profiling is improved and a standardized speed test script is included
  • vg construct can accept multiple --region arguments for different contigs
  • Convert GBWTGraph to GFA with vg convert.
  • VCF files with * alleles are now accepted by vg construct, and only the particular variant records with * alleles are rejected and warned about
  • Uncompressed GFA files can now be directly input (or streamed via stdin) as graphs into vg commands. (previously vg convert -g was required beforehand)
  • Karger-stein min cut alogirtm and alt proposal distribution added to vg mcmc genotyper. Scripts for performance analysis are in scripts/MCMC_makefile.sh, scripts/mcmc_dist.sh.
  • Count the number of nodes with self-loops with vg stats.
  • vg srpe has been removed
  • vg mod options --kill-labels and --strong-connect have been removed.
  • vg stats -L counts self-loops.
  • vg stats -e lists nondeterministic edge sets.
  • vg find option --mapping enables finding nodes that map to the selected ids.
  • vg is now able to build bundled htslib on Autoconf 2.70+

New and Updated Submodules

The fermi-lite, gbwt, gbwtgraph, 'gcsa2', gfakluge, jemalloc, libvgio, and sdsl-lite submodules have been updated.

Make sure to git submodule sync and git submodule update --init --recursive if building from source. The jemalloc update is also known to not build over top of a previous built version; you may need to rm -Rf deps/jemalloc and git submodule update --init --recursive to fix it in your copy.

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