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@jeizenga jeizenga released this 04 Aug 18:04
· 5850 commits to master since this release
v1.26.0
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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:v1.26.0

Buildable Source Tarball: vg-v1.26.0.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 gbwt -a adds a path cover of components without haplotypes to an existing GBWT. This resolves the Giraffe issue with a large number of incorrect mapq 60 reads in some graphs with the full GBWT.
  • New seeding algorithm targeted at miRNA
  • More flexible build system
  • Pangenome ontology now has linkZoomLayer
  • Synchronized semantics for OVERLAP_THRESHOLD
  • Chopping with mod -X changed to run natively on handle graphs
  • vg stats -F prints graph format
  • Major vg index refactor.
  • Always build GBWT from a single graph with a single thread source (VCF, GAM, GAF, paths).
  • Index embedded paths as samples instead of contigs with vg index option --paths-as-samples.
  • Correct names for long options in vg gbwt.
  • Ignore metadata in empty indexes when merging GBWTs.
  • add vg stats -D option to print degree distribution
  • GAM/GAF I/O code moved into libvgio
  • Ability to specify contig ploidy in vg sim
  • Alignment with dozeu can now handle large full length bonuses without crashing
  • dozeu is now non-x86 compatible.
  • Made match pruning in mpmap less aggressive for very short reads
  • mpmap can now use the distance index's algorithm for rescue graph extraction
  • mpmap now can use the distance index in place of a snarl manager to guide the structure of multipath alignments
  • Better vg map error message when xg input not found
  • GBWT construction from GAM/GAF is faster and handles duplicate read names correctly.
  • vg sim can now output a table of the path positions that reads were simulated from
  • Added a subcommand gampcompare to evaluate mapping correctness of multipath alignments
  • libvgio now only tries to find Protobuf once
  • Memory should no longer blow up in mpmap on splice-abundant graphs
  • GaplessExtender returns all non-overlapping full-length extensions.

New and Updated Submodules

The gssw submodule is pointing at a different repository. Use git submodule sync to update the pointer if building from source.

The libvgio, dozeu, gbwt, libbdsg, gssw, structures, and gbwtgraph submodules have been updated.

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

Assets 4
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