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vg 1.78.0 - Sharptooth

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@parsaeskandar parsaeskandar released this 19 Oct 18:37
· 841 commits to master since this release
v1.78.0
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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:v1.78.0

Buildable Source Tarball: vg-v1.78.0.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 giraffe chaining mode removes overlapping chains from multiplicity calculation (bumps reads to higher MQ)
  • make clean no longer rebuilds from complete scratch, and its test isn't in test/t
  • vg no longer computes M5 SAM/BAM tags from reference paths in the graph, or validates them in incoming sequence dictionaries. This is so you can surject reads to GRCh38 with IUPAC codes changed to N (the only way it can exist in a vg graph), and then use the resulting SAM/BAM files with GRCh38 as released, without tools complaining that the reference sequences don't match.
  • Bash-TAP tests should no longer leave so many scratch files behind.
  • vg JSON input code can now detect end-of-file properly.
  • Deprecate vg viz
  • vg view -d emoji/color combos chosen on path basenames without considering subranges (resolves #5038)
  • PackedGraph construction now faster (ex vg convert g.gfa > g.vg)
  • Special haplotype sampling logic added for "gref" references. Base contigs are fixed, but "alt" contigs can be clipped or lost.
  • Calling code is now split into more or less one header file per class.
  • vg chunk -H/--haplotype-paths includes haplotype paths in graph chunks (works on GBZ and non-GBZ input)
  • vg's Makefile now supports --dry-run and --dry-run --always-make (and includes the required Automake workarounds for dependencies)
  • You can now make compile_commands.json to get a compile commands database for editor tooling.
  • Support for GAF v1.1 with a reference-free representation of mismatches and deletions in difference strings.

Updated Submodules

  • Updated submodules gbwt, gbwtgraph, libbdsg, and libvgio

New Submodules

Removed submodules

Assets 5
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