vg v1.76.0 - Chomper

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.76.0

Buildable Source Tarball: vg-v1.76.0.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 now builds with GNU Make 4.4.1, as on Ubuntu 26.04
• vg now uses system libelf/libdw
• vg now ships its own Cairo and pixman libraries as submodues, to enable static builds on modern Ubuntu. These build with Meson; if needed, a new enough Meson will be installed on older Ubuntu via pipx by make get-deps.
• Reverted #4926 due to crashes in the compiler in the emulated builds
• vg Docker containers are now built on top of Ubuntu 26.04
• Deprecated subcommands removed: vg sift, vg join, vg explode
• Smoother interface & errors for vg circularize; vg circularize --describe is removed (use vg paths --list instead).
• Unit tests no longer use vcf2tsv and fastahack
• Add hub labeling to distance index, which allows efficient exact shortest distance queries even in "oversized" snarls
• Bug fix for minimizer, significant speed improvement
• Update bash autocomplete files, and force them to remain up-to-date
• vg giraffe now validates more options, including pairs of options describing min and max values of ranges
• Descriptive error when creating a graph from FASTAs with duplicate names
• vg snarls --path-prefix helptext no longer borked
• vg now uses a more current bundled vcflib
• Remove oodles of unused code without change to functionality
• vg map --buffer-size is hidden (it wasn't doing anything anyhow)
• vg stats --to-tail helptext now says "tail" instead of "head"
• vg filter --tsv-out can output PHRED base quality scores (lets us get rid of xxd dependency in tests)
• Added GFAz input support to vg
• vg view hint no longer makes it seem that it only takes .vg
• Interactive chaining dotplots no longer mix minimizer pin point and anchor start positions
• When reading in a GFA, node sequences are normalized (uppercased, non-ACGT converted to N) even if not strictly required for output format
• No more overlap in vg help output (fix regression due to new subcommand)
• Minor README polish
• vg can now build on Mac systems with htslib 1.24+ installed via Homebrew; no longer lets system htslib replace the vg-vendored version on accident
• vg msga is removed; see the vg wiki for how to create a graph from sequences with alignment and vg augment, or use Minigraph-Cactus or PGGB instead.
• Fix make clean and put under CI test
• Add --cluster-min-len option to vg deconstruct that sets threshold for when allele-merging (-L) is applied
• vg call errors about not finding reference paths are more descriptive
• vg stats -R --snarl-sample more robust for reverse-strand or chopped up references.
• GFAz input now uses GFAz’s public streaming decoder API, including support for unseekable input streams. This follows up on #4861 and moves the remaining GFAz format interpretation out of vg.
• scripts/chunked_call prints out a deprecation warning
• vg paths -N removed. There is now only one way to make gref paths, with -u and this auto-assigns the name to gref_<REF_SAMPLE>
• The simpler naming scheme is used by deconstruct and call to not make confusing vcfs with both base reference and gref references inside

Updated Submodules

• Updated submodules gbwt, gbwtgraph, libbdsg, libvgio, sparsehash, sparsepp, structures, and vcflib

New Submodules

• Added submodules cairo, pixman, and GFAz

Removed submodules

• Remove submodules elfutils, fermi-lite, libVCFH, and snappy