vg 1.63.0 - Boccaleone

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.63.0

Buildable Source Tarball: vg-v1.63.0.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:

• Add a man page (make doc/man/vg.1, https://github.com/vgteam/vg/wiki/vg-manpage)
• Better description of how to use input options for types of JSONs in vg view
• Since vg rna can't parse .gz files, have it give a useful error for those inputs
• Long Read Giraffe is now in vg. The vg giraffe subcommand now supports long reads.
  • vg giraffe now has --parameter-preset hifi and --parameter-preset r10 for using a new chaining-based algorithm to map long reads. --parameter-preset chaining-sr uses the new algorithm for single-ended short reads; the old --parameter-preset default and --parameter-preset fast remain available with the old non-chaining algorithm for short reads or paired-end inputs.
  • giraffe-facts.py script now knows how to read GAM files internally and no longer needs JSON preprocessing.
  • The vg giraffe minimizer file format has changed.
  • There is also a new .zipcodes index file used in vg giraffe mapping.
  • Improvements have been made to the distance index format used in vg giraffe.
• Haplotype information files used in haplotype sampling are a bit smaller. Existing files can still be used.
• Allow selecting the identity field in vg filter --tsv-out
• vg giraffe, vg mpmap, and vg map will now fail early with an error when encountering a read with a quality string of the wrong length (as from a truncated FASTQ)
• vg now tries to limit itself to a good number of threads for the number of CPUs in any enclosing Slurm job, via SLURM_JOB_CPUS_PER_NODE and CPU affinity masks.
• vg chunk can now properly take a chunk of a path that already has a subrange
• vg inject now has --add-identity to calculate 'identity' statistic (e.g. for linear mapper output BAMs)
• Add vg primers to get stats about variants in PCR primers from primer3
• Stop identity() from penalizing soft clips (insertions at start/end of path) as part of the total length
  • Note that this changes calculation used for the identity field in GAM files!
• vg autoindex will no longer duplicate input gbz as .giraffe.gbz when indexing for Giraffe.
• GAF sorting with vg gamsort is much faster than before.

Updated Submodules

The dozeu, gbwt, gbwtgraph, libbdsg, libhandlegraph, libvgio, and sublinear-Li-Stephens submodules have been updated.