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@adamnovak adamnovak released this 22 Jun 22:13
· 4593 commits to master since this release
v1.25.0
a393b48
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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:v1.25.0

Buildable Source Tarball: vg-v1.25.0.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:

  • New development in vg mcmc
  • Graph Alignment Format (GAF) output support for vg map and vg giraffe
  • Revisions to distance index format; distance indexes will need to be rebuilt
  • STL-based multipath alignment internal format
  • Bugfixes to Integrated Snarl Finder
  • Improvements to dozeu alignment algorithm
  • Bugfixes in banded global aligner algorithm
  • CI tests rearranged into batches
  • Bugfix for slow clustering in vg giraffe
  • Parallel snarl finder in vg deconstruct
  • Bugfixes to NetGraph in the absence of unary snarls
  • Update to XG encoding
  • Transfer mapqs when converting multipath alignments
  • Bigger bins for coverage stats in vg call
  • Better write parallelism in mpmap
  • Case insensitivity for some mapper option values
  • Fix build of SNarlManager with latest Protobuf which prohibits inheriting from messages
  • Find the missing start indexes on multipath alignments
  • New default gbwt id interval value in vg rna
  • Renamed vg gaffe to vg giraffe
  • Avoid out-of-bounds CNV and inversion breakpoints when generating random test graphs
  • Bugfixes to variant caller
  • Disqualify ultrabubbles with tips
  • Fix vg rna crash when using reverse embedded paths
  • Improvements to vg sim read simulation, especially for microRNA
  • Don't enter infinite loop in vg sim when simulating from short paths
  • Reduce information copying on multipath alignments
  • Changed default vg giraffe parameters and added a fast mode
  • Fix incorrect assert in vg sim
  • Fix presets in vg mpmap
  • Made clustering distance limit adjust itself for longer read lengths for vg giraffe
  • Fix missing metadata for multipath alignments
  • Added vg call option to output traversals to gentoype with rpvg
  • Update CI to latest toil-vg
  • Better Giraffe rescue
  • Ploidy option for vg deconstruct
  • Fix annotation boundary bug in vg rna
  • Added -T option in vg call to pad traversals
  • Added overlap threshold in GaplessExtender to deduplicate nearly identical vg giraffe results
  • New seeding algorithm in vg mpmap targeted at miRNA

New and Updated Submodules

The gbwtgraph and xg, submodules have been updated.

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

Assets 4
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