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@Robin-Rounthwaite Robin-Rounthwaite released this 01 Jul 18:54
· 6965 commits to master since this release
v1.17.0
aa0b378
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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:v1.17.0

Buildable Source Tarball: vg-v1.17.0.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 annotate edited to search further for path hits.

  • Single-ended Dijkstra algorithm factored out into its own HandleGraph algorithm.

  • HandleGraphs can be loaded from files with dynamic implementation selection

  • Fixed bugs in minimum distance clustering

  • Fixed bugs in AlignmentEmitter

  • vg gaffe improved speed and memory

  • GBWT manipulation tools in vg gbwt

  • vg mod -i deprecated, replaced by vg augment -i

  • vg edit mostly refactored into augment.cpp, except for the interface with lists of paths.

  • 'vg find -E' extracts nodes with an id range defined by a path interval.

  • vg convert allows graph type conversion between graph implementations.

  • vg gbwt now considers unphased homozygous variants as phased to prevent phase breaks. This can be disabled with option -z.

  • Improved vg compilation on MacOS with gcc 9

  • pack -q allows weighting support by mapping quality.

  • Bug fixed in split strand overlay

  • Bug fixes with compilation errors using G++ 9.1.0.

  • Bug fix in tcmalloc.

  • Speed up vg filter

  • vg call now supports pack graph format.

  • xg moved into vg namespace.

  • vg call can now call sites in parallel.

  • Names added to transcripts written to the gbwt index. Transcript naming has been simplified.

  • gam output option from gbwt is removed. Gam files can be generated from gbwt transcript index using vg paths.

  • Small speed-up for merging packer objects in vg pack.

  • Options added for adding either reference paths or non-reference paths as embedded paths in a graph.

  • vg deconstruct now works with more input graphs.

  • PackedGraph and HashGraph now moved to sglib.

  • vg paths -F now writes embedded paths in FASTA format.

  • Factored out path-to-component index from XG

  • Bug fix in rewrite_segment.

Assets 4
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