Skip to content

vg 1.64.0 - Vibbiana

Choose a tag to compare

View all tags
@adamnovak adamnovak released this 10 Mar 19:13
· 762 commits to master since this release
v1.64.0
7acd56a
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

Download for Linux

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.64.0

Buildable Source Tarball: vg-v1.64.0.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:

  • vg giraffe logs now include more information about candidate chains.
  • vg find -r will no longer include empty nodes for nonexistent node IDs in the range being extracted.
  • TLEN for read 1 starting inside read 2 will no longer be shorter than the union of the reads in vg surject.
  • TLEN computation handles more CIGAR operations in case we decide to use them.
  • vg chunk now outputs and accepts base path ranges.
  • vg giraffe has new hifi and r10 preset parameters that improve speed, are mostly neutral on calling accuracy, but add more wrong MAPQ 60 HiFi reads.
  • Zip code ancestor orientation bugfix for vg giraffe: all minimizer and zipcode files will need to be re-generated to take advantage of it.
  • GFA L-lines now written before P/W lines when converting to GFA (using vg's own implementation). The main upshot is that paths in the output of vg convert -fW can now be viewed in BandageNG.
  • Giraffe now rebuilds both the minimizers and zipcodes if either needs to be rebuilt
  • Loading an old minimizer file now fails
  • Haplotype sampling can sample fragmented haplotypes in large snarls.
  • vg man page now includes options hidden behind --help.
  • Wiki pages for long-read Giraffe are now under CI testing
  • vg giraffe should no longer produce final mappings with nonzero offsets or other wrong answers when a read tail doubles back on itself.
  • GBWTGraph GFA parsing algorithm can handle missing SeqStart/SeqEnd fields in W-lines.
  • Reference samples for haplotype sampling can be selected with --set-reference in vg haplotypes and vg giraffe.
  • vg giraffe can now handle self-loop cycles that happen to fall exactly where it wants to put an all-insertion edit.
  • vg giraffe allows multiple tips for anchor nodes if they are the same length and back-translation can work.
  • vg giraffe should no longer find and be very confident in obviously insignificant rescue alignments for paired reads.

Updated Submodules

The gbwt and gbwtgraph submodules have been updated.

Assets 5
Loading