vgteam/vg: vg 1.71.0 - Cera

Don't forget to mark the static binary executable: chmod +x vg Docker Image: quay.io/vgteam/vg:v1.71.0 Buildable Source Tarball: vg-v1.71.0.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: Running vg augment with no arguments will print helptext Recombination aware chaining fixes Explainer explanations for reads now get organized into explanation_<READ_NAME> directories. Explainer explanations for reads now explain all chains, not just the best one. Explainer explanations for reads now include coordinates on all haplotypes, not just references. New scripts/plot_chains.sh script to plot all the chains for explained reads against all the contigs GBZ graphs store stable graph names (pggname). The information is copied to haplotype information files, minimizer indexes, and GFA/GAF headers. Some subcommands (e.g. vg giraffe, vg haplotypes, vg pack) use the information to determine if the input files are compatible. Standalone GBWTGraph (.gg) files are no longer supported. New version of haplotype information (.hapl) files with tags. Old files can still be read. Haplotype sampling should work better with noisy kmer counts. Bugfix for vg giraffe chaining; improvements to accuracy and minor effect on runtime Add option vg haplotypes --ban-sample vg filter gives a clean error when passing files that don't look like GAMs vg paths prints a warning if path criteria select 0 paths vg gbwt and vg autoindex support GFA files with grammar-compressed walks. Random double space in a vg autoindex logging line is now a single space The random zip code tree test works with the --rng-seed option. -P option added to vg snarls and vg index to specify a reference backbone for orienting the snarl tree. This can be required to run vg haplotypes on some graphs from minigraph-cactus with newer vg versions. Can be thought of as a much higher-level version of the current -w interface which lets you manually upweight nodes. Updated Submodules gbwt gbwtgraph libvgio