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@xchang1 xchang1 released this 27 Sep 18:43
· 2712 commits to master since this release
v1.35.0
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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:v1.35.0

Buildable Source Tarball: vg-v1.35.0.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:

  • Multipath alignments from vg mpmap are more decomposable in tails near soft clip
  • Giraffe does not attempt rescue if it would be too slow.
  • vg gamcompare can use distances from a distance index instead of path position annotations.
  • Fix bug in vg chunk -T where input path ranges were incorrectly used to find subgraph size.
  • Fix GAF parsing bug that caused memory explosion for long paths.
  • Fix vg augment -B to not initialize packer object unnecessarily.
  • surject joins deconstruct in supporting vg subpath naming, but path lengths must come from --ref-paths in order to be valid in the output header.
  • deconstruct AT INFO field fixed to have Number=R instead of A
  • vg mpmap has improved sensitivity for detecting spliced alignments and ability to use genome-derived splicing statistics for non-humans
  • vg surject -S no longer crashes if it decides that a deleted/spliced segment is too long to realign.
  • vg autoindex can handle VCFs that list contigs for which there are no variants
  • Giraffe now shuffles tied top read mapping candidates like mpmap and map, to avoid arbitrary biases
  • vg sim now produces more realistic RNA-seq fragment length distributions.
  • libbdsg dependency should no longer sometimes fail to build on a clean checkout due to missing mio/mmap.hpp\
  • Tail alignments can no longer skip read sequence completely when alignment would be too large
  • Giraffe progress reports now include fragment length distribution information
  • Giraffe can now find .giraffe.gbz GBZ files automatically.
  • vg pack gets new -s option to ignore first and last N bases of reads. -s 5 works well in practice for SV genotyping.
  • vg call default parameters re-tuned to work a bit better on complex graphs. An extra filter for completely unsupported breakpoints is added to increase precision.
  • libvgio now uses a simpler CMake build
  • vg call -e now works again
  • CI testing now uses Toil 5.4.0
  • vg rna now supports using GBWT haploytypes as reference paths (--use-hap-ref option).
  • vg rna can now create a spliced pangenome graph and pantranscriptome with chopped nodes (--max-node-length option).
  • Spliced pangenome graphs and pantranscriptomes can be sorted and have their ids compacted in vg rna (currently only works for inputs in the PackedGraph format).
  • The transcript haplotype info table from vg rna no longer contains the "Reference" column (is part of the "Haplotypes" column now).
  • The names for the options --use-all-paths and --add-non-ref-paths in vg rna have been changed (single-letter option the same) and the option --gbwt-id-interval has been removed (not relevant anymore).

New and Updated Submodules

  • libbdsg and libvgio have been updated.

Make sure to git submodule sync and git submodule update --init --recursive if building from source.

Assets 4
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