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@adamnovak adamnovak released this 04 Dec 18:38
· 3729 commits to master since this release
v1.29.0
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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:v1.29.0

Buildable Source Tarball: vg-v1.29.0.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:

  • XG indexing now uses the temporary directory also for SDSL temp files.
  • New GBWT construction interface in vg gbwt.
  • vg mpmap now can perform multiple spliced alignments on one read and spliced alignments on multiple mappings.
  • Update to latest vcflib ("Configure for default, libcurl-using HTSLib config") to get non-x86 support
  • Cross building for other architectures is now easier due to the use of $PKG_CONFIG for specifying pkg-config binary
  • SAM/BAM/CRAM TLENs should now match BWA's for identical alignments
  • Remove multiple samples with vg gbwt -R.
  • Mac builds on Catalina no longer fail with a "missing separator" error.
  • CIGAR strings in SAM/BAM/CRAM should now consistently coalesce runs of adjacent insertions and deletions.
  • Readme no longer encourages using the unsupported GNU GCC build on Mac.
  • Spliced multipath alignments are strand consistent and have a more complete representation of variation near splice sites.
  • vg filter can now work on GAMP files with -M, and reads with a given subsequence can be filtered with -a and -A.
  • vg mod -n should now work properly when self loops happen at the ends of merged nodes
  • CIGAR strings for spliced surjection from GAM files now have correct intron lengths
  • CI now tests macOS 10.15
  • vg now uses (and needs!) system Boost for Vowpal Wabbit instead of bundling a subset
  • Parallel GBWT merging algorithm in vg gbwt.

New and Updated Submodules

The gbwt, mmmultimap, vcflib, vowpal_wabbit, and xg submodules have been updated.

The source repository for the vowpal_wabbit submodule has moved.

The boost-subset submodule has been removed.

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

New dependencies

Instead of shipping a subset of Boost, vg now requires Boost to be installed on the system already in order to build.

Assets 4
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