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@adamnovak adamnovak released this 21 Nov 17:31
· 2540 commits to master since this release
v1.44.0
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Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.44.0

Buildable Source Tarball: vg-v1.44.0.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:

  • GAF output fixed to 1) no longer have consecutive deletions in the CIGAR and 2) be valid for split mappings within the same node (which can happen when mapping long reads with vg map)
  • vg autoindex can auto-tune some key indexing parameters for increased robustness.
  • vg autoindex no longer crashes on VCFs that contain no samples.
  • Add the flag --num-bp-per-min to Giraffe to adjust the number of selected minimizers based on the read length.
  • vg main GFA loader can now handle HPRC-style GFAs where the same path exists as rGFA tags and P lines.
  • L-lines in GFA output changed back to have 0M cigars (reverting switch to * in v1.31.0)
  • vg surject can annotate SAM/BAM records by all of the sequences it attempted to realign to
  • vg surject has improved stability on cyclic graphs
  • Handle GBWTGraphs and GBZ graphs that do not contain a translation correctly when a translation is needed.
  • vg construct will no longer fail with an assertion error about last_edit_end != -1 and will instead report the variants that confused it.
  • vg construct will skip over and warn about variants that do not actually change anything.
  • vg should now only link one copy of Protobuf into the non-static build
  • vg should now build against newer libomp from Homebrew which is keg-only
  • vg rna now support reference transcript paths where exon boundaries are on opposite strands
  • vg convert --drop-haplotypes will drop haplotype paths from the output graph.
  • preliminary GBZ input support in vg deconstruct and vg call
  • vg surject, vg giraffe, vg mpmap, vg filter, and vg deconstruct now accelerate paths-on-node queries with an overlay, so working from a GBZ will no longer be quite as slow relative to working from an XG
  • libbdsg PackedReferencePathOverlay should no longer crash for short paths
  • Update distance index to distance index 2 to be more efficient and make clustering faster
  • Minimizers now have a payload with two ints
  • DI2 files will need to be rebuilt as well as minimizers that use the distance index
  • New vg chunk option -S can be used to extract every snarl that is fully contained in the the given path region (ie specified with -p). This can be used instead of context steps -c. The advantage is that -S will return everything inside the region and nothing outside the region (barring the start and end nodes), which helps with the problem of pulling out massive amounts of neighbouring regions when jacking up -c for complex subgraphs. The disadvantage is that if the region specified contains only parts of snarls, the results will be a misleadingly simple graph.
  • vg viz no longer silently fails when asked to draw a PNG that is too big for Cairo

Updated Submodules

The gbwt, gbwtgraph, gcsa2, libbdsg, libhandlegraph, libvgio, and xg submodules have been updated.

Assets 4
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