vg 1.45.0 - Alpicella

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.45.0

Buildable Source Tarball: vg-v1.45.0.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 now removes edges not meeting the depth threshold, in addition to nodes
• vg paths -C reports both undirected (visit any node twice) and directed (visit any node twice in same orientation) cyclicity
• Macports-based installation instructions have been simplified
• vg Mac build now works even if g++ --version doesn't actually have the version string on the first line
• vg no longer supports the "ODGI" format. The implementation that vg used was never compatible with the implementation in the actual odgi tool. If you have graphs in the old vg-odgi format, use vg 1.44.0 to convert them to another format. To exchange data with the odgi tool, use the GFA format.
• Fix stats -p option
• vg giraffe --align-from-chains invokes a separate (still experimental) long-read-optimized codepath.
• vg giraffe option parsing uses a new setup that makes it easier to add and report on options.
• Giraffe funnel explanations can track correctness and placed-ness along the length of a read.
• vg mpmap has increased sensitivity for detecting splice junctions
• vg autoindex can produce graphs (included spliced graphs) from FASTAs without requiring VCFs
• vg autoindex now splits the indexing for vg mpmap from the indexing for rpvg. The previous behavior can be recapitulated by indicating both workflows: --workflow mpmap --workflow rpvg
• vg chunk and vg trace can now get haplotypes from an input GBZ file
• vg chunk can use --no-embedded-haplotypes to ignore haplotypes from a GBZ.

Updated Submodules

The libbdsg and libhandlegraph submodules have been updated.

vg 1.44.0 - Solara

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.44.0

Buildable Source Tarball: vg-v1.44.0.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:

• GAF output fixed to 1) no longer have consecutive deletions in the CIGAR and 2) be valid for split mappings within the same node (which can happen when mapping long reads with vg map)
• vg autoindex can auto-tune some key indexing parameters for increased robustness.
• vg autoindex no longer crashes on VCFs that contain no samples.
• Add the flag --num-bp-per-min to Giraffe to adjust the number of selected minimizers based on the read length.
• vg main GFA loader can now handle HPRC-style GFAs where the same path exists as rGFA tags and P lines.
• L-lines in GFA output changed back to have 0M cigars (reverting switch to * in v1.31.0)
• vg surject can annotate SAM/BAM records by all of the sequences it attempted to realign to
• vg surject has improved stability on cyclic graphs
• Handle GBWTGraphs and GBZ graphs that do not contain a translation correctly when a translation is needed.
• vg construct will no longer fail with an assertion error about last_edit_end != -1 and will instead report the variants that confused it.
• vg construct will skip over and warn about variants that do not actually change anything.
• vg should now only link one copy of Protobuf into the non-static build
• vg should now build against newer libomp from Homebrew which is keg-only
• vg rna now support reference transcript paths where exon boundaries are on opposite strands
• vg convert --drop-haplotypes will drop haplotype paths from the output graph.
• preliminary GBZ input support in vg deconstruct and vg call
• vg surject, vg giraffe, vg mpmap, vg filter, and vg deconstruct now accelerate paths-on-node queries with an overlay, so working from a GBZ will no longer be quite as slow relative to working from an XG
• libbdsg PackedReferencePathOverlay should no longer crash for short paths
• Update distance index to distance index 2 to be more efficient and make clustering faster
• Minimizers now have a payload with two ints
• DI2 files will need to be rebuilt as well as minimizers that use the distance index
• New vg chunk option -S can be used to extract every snarl that is fully contained in the the given path region (ie specified with -p). This can be used instead of context steps -c. The advantage is that -S will return everything inside the region and nothing outside the region (barring the start and end nodes), which helps with the problem of pulling out massive amounts of neighbouring regions when jacking up -c for complex subgraphs. The disadvantage is that if the region specified contains only parts of snarls, the results will be a misleadingly simple graph.
• vg viz no longer silently fails when asked to draw a PNG that is too big for Cairo

Updated Submodules

The gbwt, gbwtgraph, gcsa2, libbdsg, libhandlegraph, libvgio, and xg submodules have been updated.

vg 1.43.0 - Barisano

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.43.0

Buildable Source Tarball: vg-v1.43.0.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:

• Mac CI now runs on MacOS 12
• uniform_int_distribution unit tests no longer hang on MacOS 12
• vg giraffe can now --align-from-chains to do long-read alignments
• Makefile now supports make bin/unittest/<test_file_name> to build a dynamically-linked binary for just one file of unit tests, for faster iteration.
• -c option added to vg depth path coverage in order to count each time a path steps on a position. By default vg depth continues to only count each path once

Updated Submodules

The vcflib submodule has been updated.

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.