vg 1.62.0 - Ranzano

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.62.0

Buildable Source Tarball: vg-v1.62.0.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:

• GBWT construction from a GAM/GAF file now uses parallel construction jobs.
• vg chunk and vg find now generate subpaths with subrange metadata when cutting up paths.
• vg gbwt will accept subranges on fragment 0 and discard the fragment number.
• vg map, vg mpmap, and vg giraffe can now annotate output with SAM-style flags from FASTQ comments with --comments-as-tags
• vg surject now detects when multipath alignments obviously don't belong to the graph they are being surjected to.
• Updated libbdsg to check if a distance index actually has distances and to improve memory use of distance indexing when not including distances
• vg index now includes include flag --no-nested-distance to build a distance index with distances only on the top-level chain
• Add --snarl-sample to vg stats -R. This adds BED-style reference coordinates to the front of each row in the snarl output table, using the input sample to select reference paths. If no selected path is found .'s are written. If multiple paths / intervals find (in case of cyclces), the first one found is printed.
• vg deconstruct -n bug that bypassed some nested sites fixed.
• When reading a .gff3 file with vg rna, validate exon ordering by base-pair position instead of number attribute. This allows reverse-strand exons to be numbered either by base-pair order or transcription order.
• Have vg rna gracefully ignore features with bad chromosome names if they're not included in --feature-type and thus won't be parsed anyways

Updated Submodules

The gbwt, gbwtgraph, gcsa2, libbdsg, libvgio, sdsl-lite, and sublinear-Li-Stephens submodules have been updated.