Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.67.0

Buildable Source Tarball: vg-v1.67.0.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:

• GAF path end positions are calculated correctly in some edge cases.
• --keep-path can now be used multiple times in vg mod
• vg giraffe --track-correctness should no longer crash when read truth positions are on paths that exist in the graph, but are too short to reach where the read is.
• Bring vg cluster up-to-date: now accepts GBZ files, can do short-read or long-read giraffe, and allows --prefix for better compatibility with vg autoindex
• Add some options to vg cluster to help with chaining issue diagnosis: print out cyclic snarl sizes, seeds with high hit amounts
• Fix GFA haplotype sniffing for GFAs with P-lines
• Use graph metadata and not path name to determine reference/haplotype status for paths in vg call and vg deconstruct.
• Loading transcript files will now produce a human-readable error message when there are duplicate transcripts with the same ID on different paths.
• The GBWT built while sorting GAF with vg gamsort is now forward-only by default.
• vg sim now can output in FASTQ format via --fastq-out
• Make vg mod -t take an argument and stop -E from requiring one
• In vg chunk, fix the long names for -P, -c, -r, and -R, and make the latter two accept arguments.
• Register command line options correctly & put them under test (scripts/check_options.py). This involved a lot of minor bugfixes and helptext modifications, collected in a Google Doc.
• Manually wrap option helptext lines after 80 characters
• vg sim now works with sample name even when no GBWT is provided.
• CI now enforces the minimum required GCC version.
• vg now requires a minimum GCC version of 7, the oldest major version available in the Ubuntu releases we test on for CI.
• vg giraffe usage example now shows using a .zipcodes file and a .withzip.min file.
• vg can now be built with the mimalloc allocator (v3 beta)

Updated Submodules

• BBHash
• libbdsg
• libvgio
• sdsl-lite
• sparsepp
• vcflib

New Submodules

• mimalloc

Removed Submodules

• fastahack (now used via vcflib)