vg 1.42.0 - Obolo

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.42.0

Buildable Source Tarball: vg-v1.42.0.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 releases should now have their Docker containers built by our CI.
• vg releases should now have ARM/amd64 multiarch Docker tags.
• README now documents using Giraffe.
• SAM/BAM alignment output and surjection now tries to use reference paths, and then generic paths, but won't use haplotype paths by default

Second DOI release for pantranscriptomics paper

This is a non-versioned release created in order to make a stable DOI for the source code to support reproducibility in the VG pantranscriptomics paper.

vg 1.41.0 - Salmour

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.41.0

Buildable Source Tarball: vg-v1.41.0.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 inject will report an error when paths don't exist in the graph, instead of doing undefined behavior.
• vg now has metadata for paths; haplotype paths can now exist in places other than a GBWT. Try vg paths -M -x <graph> on a vg, GFA, or GBZ file to see it.
• vg convert now has a --ref-sample option for promoting a haplotype to a reference during conversion.
• vg gbwt and vg index no longer have --paths-as-samples; prepare input with paths of the appropriate senses instead.
• vg will interpret W lines in input GFA files as haplotypes
• vg will interpret W lines with * as the sample name as generic named paths.
• vg will interpret PanSN P line names in input GFA files as haplotypes
• vg will interpret PanSN P line names with #<number> after them as (pieces of) haplotypes
• vg will interpret string-type RS tags in GFA headers as space-separated lists of samples whose paths are references, not haplotypes.
• vg will generate GFA files using W lines for reference and haplotype paths, and containing RS header tags to distinguish them.
• vg surject preserves group MAPQ annotations from vg mpmap as "GM" tag.
• vg mpmap's secondary alignment annotations are preserved by vg surject
• vg gbwt can now manipulate GBWT tags and change reference samples in a GBWT or GBZ, as documented on the wiki.

Updated Submodules

• gbwtgraph
• libvgio
• libbdsg
• dozeu
• gfakluge (removed)

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

vg 1.40.0 - Suardi

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.40.0

Buildable Source Tarball: vg-v1.40.0.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:

• README now explains how to migrate to ARM Macs
• vg mpmap now distinguishes unmapped reads from reads with MAPQ 0
• vg mpmap is faster on very complex cyclic graphs
• vg chunk -m no longer bothers parsing Alignments
• vg sim will stop if there are too many Ns in the source graph instead of spinning forever

Updated Submodules

• libzstd
• libbdsg
• xg

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

vg 1.39.0 - Runzi

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.39.0

Buildable Source Tarball: vg-v1.39.0.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:

• CI now uses Toil compatible with pip 22.
• vg giraffe can now produce GAF using GFA segment name coordinates.
• vg sim no longer annotates reads with positions along synthesized haplotype paths
• vg sim supports --multi-position option of vg annotate, for annotating simulated reads with path positions per node.
• vg gbwt supports --pass-paths option to use paths from a passed-in graph when computing a path cover or local haplotype cover GBWT.
• vg sim supports simulation from a set of HSTs in a pantranscriptome from vg rna
• vg giraffe supports annotating reads with coverage by minimizers that gave rise to correct seeds.

Updated Submodules

• gssw
• libvgio

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

vg 1.38.0 - Canossa

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.38.0

Buildable Source Tarball: vg-v1.38.0.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:

• JSON GAM quality string representation of base64-encoded PHRED+0 is now under test
• vg deconstruct now uses OMP tasks instead of nested parallel sections, which caused problems keeping threads caches straight.
• vg giraffe --output-basename is respected again
• Multithreaded GBWT / GBZ construction from GFA in vg gbwt.
• Multithreaded GBZ / GBWTGraph to GFA conversion in vg convert.
• make clean now works on submodules that lack top-level Makefiles
• vg now builds with GCC 11
• vg giraffe --named-coordinates can produce GAM output with positions in the space of the input GFA, for indexes produced from a GFA with vg autoindex.
• CI jobs that use Docker builder deployment now stop early if they don't see it.
• vg autoindex supports --gbwt-buffer-size to increase the buffer size for indexing long haplotypes.
• vg snarls now supports --named-coordinates for reporting snarls and snarl traversals in input GFA coordinates.
• vg mpmap produces more accurate and parsimonious alignments on complex graphs

Updated Submodules

• elfutils
• gbwtgraph
• gssw
• libbdsg
• libhandlegraph
• libvgio
• sdsl-lite
• structures
• vcflib

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

vg 1.37.0 - Monchio

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.37.0

Buildable Source Tarball: vg-v1.37.0.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 clip -D fixed to do a better job breaking up giant snarls.
• Option -A added to vg call to call all snarls, including child snarls (analagous to vg deconstruct -a)
• Options -c and -C added to vg call to restrict snarl calling to sites within specified size range
• vg construct -a no longer generates, and other vg tools no longer expect to see, empty paths for some variants
• The segment translation table can be extracted from a GBZ file with vg gbwt.
• vg autoindex no longer calls out-of-scope lambdas captured by reference
• vg call VCF output now more consistent with vg deconstruct: LV and PS tags are added (with -A), snarl names in variant IDs are written the same, and the AT tag is added. -N option added (equivalent to -T in deconstruct) to apply a node translation table.
• vg call GAF output (-T/-G) more informative, with positional information stored in the names and (individual) read support for each allele with the AD optional tag
• .gbz files can now be used anywhere a graph with embedded paths is expected.
• vg autoindex will embed graph paths into Giraffe GBWT and GBZ files.
• vg giraffe will now use the GBZ file for output on a linear reference and no longer needs an xg.
• vg giraffe will prefer to use named paths from an XG, if available, over those in a GBZ.
• Prevents buffer size errors in GBWT creation by vg autoindex

Updated Submodules

• gbwt
• gbwtgraph
• gssw
• libbdsg
• libhandlegraph
• libvgio

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

DOI release for pantranscriptomics paper

This is a non-versioned release created in order to make a stable DOI for the source code to support reproducibility in the VG pantranscriptomics paper.

vg 1.36.0 - Cibottola

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.36.0

Buildable Source Tarball: vg-v1.36.0.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:

• Builds again on Ubuntu 18.04
• Giraffe records read and pair mapping wall clock times
• Giraffe can no longer output fragment length annotations too large to convert from JSON to GAM
• Giraffe no longer uses duplicate minimizers as often for seeds, potentially increasing mapping speed.
• Giraffe --track-provenance will no longer crash when considering improperly paired mappings
• Surjection can now prune back low-complexity or short anchors to give more-optimal alignments against the target paths (--prune-low-cplx)
• GFA file input is now checked by the parser and not just trusted to match the spec
• Mac CI Homebrew package installation is more robust
• Better handling of reversing reference paths in vg call
• Multiple -P allowed in vg clip
• vg paths messaging cleaned up to acknowledge that vg paths -E -g does indeed need a graph.
• vg giraffe and vg mpmap no longer crash when reads are in lowercase
• vg map -h should now print help again
• CI now supports secure Docker Hub mirrors
• vg call joins deconstruct and surject in transparently supporting reference subpaths
• vg deconstruct changed to write LV and PS tags wrt sites in the VCF (and will not longer reference un-exported sites from the graph)
• vg clip gets -D option for clipping out big deletion edges
• Specified --align-out parameter in vg sim as GAM-format output
• PATH is now quoted when added to

New and Updated Submodules

• gfakluge has been updated.

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

vg 1.35.0 - Ghizzano

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.