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@adamnovak adamnovak released this 23 Sep 18:00
· 7747 commits to master since this release
v1.19.0
94c19a1
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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:v1.19.0

Buildable Source Tarball: vg-v1.19.0.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:

  • The experimental vg mcmc command, a Markov-chain-Monte-Carlo genotyper prototype

  • Improved clustering and intermediate scoring logic in vg gaffe, and the elimination of MultipathAlignments from that pipeline

  • vg gaffe now emits MAPQ 0 for unmapped reads

  • Handle-graph-ification of vg map, phase unfolding, vg vectorize, vg find, vg chunk, vg call`, and other operations using the xg index. Many commands now support more file types as arguments.

  • Phase unfolder path verification no longer runs in parallel

  • A new and improved XG index implementation. Note that backward compatibility is available only for XG indexes created with vg 1.18 or newer

  • Giraffe Wrangler script now counts only mapped reads for identity computation, can take its inputs from Amazon S3, and binds BWA to a single NUMA node

  • GBWT accesses now cached

  • Giraffe Facts now reports statistics by filter instead of by mapping stage

  • Vendored Protobuf submodule has been removed. vg can now build with (and indeed now requires) system-installed Protobuf 3 from a package manager

  • vg call algorithm has been revised to use the much more efficient "pack" format, allowing much larger single calling operations

  • A paired-end clustering algorithm for use in vg gaffe has been added, but not yet used

  • Warnings about deprecated pointer types in lru_cache eliminated

  • A new Dockerfile for a multi-stage build has been integrated directly into the vgteam/vg repository. The vgteam/vg_docker repository should no longer be required.

  • The GBWTGraph has been moved to a submodule

  • Added a magic number system to identify bare XG files as XG files

  • Testing of builds of vg on Mac with GNU GCC has been discontinued. It is very difficult to get GNU GCC to build with the libc++ standard library, which packaged Protobuf builds for Mac use. GNU GCC should still work with Protobuf built with GNU GCC against its default libstdc++.

  • vg version now reports the C++ standard library used in the build

  • CFLAGS and CXXFLAGS are now honored by submodule dependencies in more (but not all) places. Some dependencies still ignore them.

  • There is now a make static-docker target which quickly builds a static vg binary in the checked-out source tree and dumps it into a Docker container

  • The build system now has its own opinion about whether the current vg binary is statically linked, as recorded by a marker file in lib/.

  • User support for vg now ought to happen on Biostars: https://www.biostars.org/t/vg/

  • Crash bug in optimal_score_on_genome has been fixed

  • Memory leaks in vg map have been plugged

New System Dependencies

Protobuf 3.0 or greater, including libraries and compiler.

New and Updated Submodules

The protobuf submodule has been removed.

The DYNAMIC, gbwt, gcsa2, gfakluge, libbdsg, libhandlegraph, libvgio, lru_cache, and sdsl-lite submodules have been updated.

The gbwtgraph, ips4o, mmmultimap, and xg submodules have been added.

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

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