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vg 1.67.0 - Vetria

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@adamnovak adamnovak released this 14 Jul 19:44
· 438 commits to master since this release
v1.67.0
379c37d
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Download for Linux

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)
Assets 5
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