vg 1.26.1 - Stornara

This is a patch release intended to serve as a the version of vg for the paper on the vg giraffe mapper.

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.26.1

Buildable Source Tarball: vg-v1.26.1.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:

• Multipath alignments have correct copy and move operators
• vg annotate -m can annotate reads with a path position for each Mapping to a node
• vg annotate now actually respects passed search limit (-l)
• Align promising partial extensions in Giraffe.
• gampcompare now returns the correct distances with the -d option
• vg mpmap -a now agglomerates multipath alignments into a single disconnected alignment (-a no longer controls the maximum alignments through a snarl)
• mpmaps MAPQ now incorporates multiplicities from cluster and alignment hard caps
• vg depth now supports GAF input
• "no sequence" mode using vg view -du where the node sequence is replaced by its size, e.g. to visualize large graphs with dot
• vg sim -E now produces correct positions in single-end simulations
• vg gampcompare output now includes a column to indicate if a read was mapped
• vg surject -S no longer produces occasional malformed BAM records
• Improved heuristic for choosing the extensions to align in Giraffe.
• New option -a for vg call includes 0/0 calls. It can help compare and merge VCFs from multiple samples called against the same graph.
• vg mpmap -a no longer crashes on read pairs that fail to find a consistent pair of mappings
• Update giraffe mapping quality caps

New and Updated Submodules

The raptor submodule has been updated.

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