Draft Changelog

This page tracks all changes since the last release of VG.

When you merge a PR, add a bullet point to this page.

When you do a release, copy the changelog from this page and clear it out.

Changes For Next Release

• 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

Updated Submodules

• gbwt
• gbwtgraph
• libvgio

New Submodules

Removed submodules