vg 1.69.0 - Bologna

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.69.0

Buildable Source Tarball: vg-v1.69.0.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.

Release Note! Compared to the previous v1.68.0 release, vg giraffe is faster on long reads, but may be less accurate for variant calling from HiFi reads, when using available trained DeepVariant models.

This release includes:

• vg inject now produces useful error messages when reads go out of range on paths
• vg autoindex now gives you hints about what files would help it, when it can't make the indexes it wants to make.
• vg chains subcommand for extracting top-level chains from a distance index or a snarls file for GBZ-base.
• vg inject will no longer spontaneously map SAM/BAM reads that have their mapping fields filled in but are flagged as unmapped.
• vg inject will now throw away scores for unmapped reads
• vg stats and vg inject can now understand reads that are asserted to be "mapped", but where the position/path is not provided, a thing the SAM spec does not appear to prohibit.
• Zip code trees for vg giraffe's chaining mode now have non-heuristic* distances in non-DAG snarls [*intra-chain reversals are still not handled at all] As a practical matter, we get significant speedups on HiFi and R10 reads (especially for the slowest reads) and a tiny increase in read identity scores (though some increase and some decrease)
• vg mapping tools can now produce supplementary alignments for SAM/BAM output
• vg giraffe now implements a recombination aware chaining algorithm
• GBWTGraph can again be built for more than 64 paths
• vg find -G now includes regions of paths touched by the extracted graph
• vg haplotypes --include-reference now also includes reference paths that do not visit any snarls.
• Breaking changes to the haplotype information (.hapl) files used by vg haplotypes. Old files can no longer be used.
• Improve automatic manpage generation
• Fixed haplotypes supported by minimizers (for recombination-aware vg giraffe)
• Add tiebreak on identity for alignments with identical score (vg giraffe)
• Heuristically detect & fix when snarl ranks are sorted backwards in zip code tree

Updated Submodules

• gbwtgraph
• sdsl-lite