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@adamnovak adamnovak released this 24 Feb 20:44
· 5517 commits to master since this release
v1.22.0
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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:v1.22.0

Buildable Source Tarball: vg-v1.22.0.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:

  • Support for haplotype transcripts and two training FASTQs in vg sim, as well as bugfixes
  • Paired-end support in vg gaffe
  • Changes to distance index format to sspport paired-end mapping. All distance indexes will need to be rebuilt.
  • Support for all PathHandleGraph implementations in most vg commands. Many commands will now output in formats other than vg Protobuf.
  • vg combine command to do what cat does for the Protobuf format when working with graphs in all formats.
  • Ability to rename variants' contigs during vg construct
  • Updates to many submodules to respect build flags, to make packaging easier
  • GFA edge orientations in output are now more canonical
  • Removal of vg stats -S and the concept of from/to-siblings
  • Addition of new predicates to the RDF ontology
  • Addition of man page for vg gaffe
  • XG edge vectorization now works correctly, which should make vg pack output and the things that use it more correct.
  • Fixed bug with vg chunk -p -C -a when not all paths are wanted in gam chunks
  • Added missing critical section in vg chunk
  • Fixed haplotype exon break bug in vg rna
  • Fixed bugs in new vg chunk gam splitting logic
  • Now vg chunk uses all threads by default
  • VPKG tag for ODGI files has been fixed. ODGI files will need to be regenerated.
  • Now filtering N's in vg augment
  • Fixed a bug with vg augment's coverage filter
  • Fixed a crash bug in vg surject built with GCC
  • Report GQ and a real QUAL in vg call
  • Magic number prefixes in SerializableHandleGraph. HashGraph and PackedGraph output will not be readable by older vg versions.
  • Fix hash graph id sorting
  • For RNA, add option to add splice-junctions from intron bed file
  • Speed improvements in vg surject
  • Fix vg augment -s option
  • Fix rare out-of-bounds index bug in vg mpmap
  • Splice support in vg surject
  • Add a collective MAPQ option to vg mpmap
  • Fix quality string in augmented GAMs
  • Ability to simulate RNA reads from haplotype transcripts
  • Support for multiple minimizer indexes in vg gaffe
  • Addition of an internal dagification overlay HandleGraph
  • Disable parallelization of second pass in vg augment
  • Do not change names of reference transcripts in vg rna
  • Fix an off-by-one error in vg surject
  • Add mpmap tests back to CI simulation tests
  • Turn on ccache for Travis CI
  • More memory efficient vg rna
  • MinimizerMapper refactoring
  • Update calibration routine for mismapping detection in vg mpmap
  • Fully ignore single-node components when doing vg snarls
  • Use the HandleGraph API in more places
  • Changes to Homebrew usage on Mac Travis CI
  • Make filters in vg filter be fully off if not requested

New and Updated Submodules

The gbwt, gbwtgraph, gssw, htslib, libbdsg, libhandlegraph, libvgio, pinchesAndCacti, sha1, sonLib, structures, vcflib, and xg submodules have been updated.

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

Assets 4
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