vg 1.37.0 - Monchio

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.37.0

Buildable Source Tarball: vg-v1.37.0.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 clip -D fixed to do a better job breaking up giant snarls.
• Option -A added to vg call to call all snarls, including child snarls (analagous to vg deconstruct -a)
• Options -c and -C added to vg call to restrict snarl calling to sites within specified size range
• vg construct -a no longer generates, and other vg tools no longer expect to see, empty paths for some variants
• The segment translation table can be extracted from a GBZ file with vg gbwt.
• vg autoindex no longer calls out-of-scope lambdas captured by reference
• vg call VCF output now more consistent with vg deconstruct: LV and PS tags are added (with -A), snarl names in variant IDs are written the same, and the AT tag is added. -N option added (equivalent to -T in deconstruct) to apply a node translation table.
• vg call GAF output (-T/-G) more informative, with positional information stored in the names and (individual) read support for each allele with the AD optional tag
• .gbz files can now be used anywhere a graph with embedded paths is expected.
• vg autoindex will embed graph paths into Giraffe GBWT and GBZ files.
• vg giraffe will now use the GBZ file for output on a linear reference and no longer needs an xg.
• vg giraffe will prefer to use named paths from an XG, if available, over those in a GBZ.
• Prevents buffer size errors in GBWT creation by vg autoindex

Updated Submodules

• gbwt
• gbwtgraph
• gssw
• libbdsg
• libhandlegraph
• libvgio

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