vg 1.63.1 - Boccaleone

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chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.63.1

Buildable Source Tarball: vg-v1.63.1.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:

• Removed unit tests for primer filtering that require the source tree

vg 1.63.0 - Boccaleone

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.63.0

Buildable Source Tarball: vg-v1.63.0.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:

• Add a man page (make doc/man/vg.1, https://github.com/vgteam/vg/wiki/vg-manpage)
• Better description of how to use input options for types of JSONs in vg view
• Since vg rna can't parse .gz files, have it give a useful error for those inputs
• Long Read Giraffe is now in vg. The vg giraffe subcommand now supports long reads.
  • vg giraffe now has --parameter-preset hifi and --parameter-preset r10 for using a new chaining-based algorithm to map long reads. --parameter-preset chaining-sr uses the new algorithm for single-ended short reads; the old --parameter-preset default and --parameter-preset fast remain available with the old non-chaining algorithm for short reads or paired-end inputs.
  • giraffe-facts.py script now knows how to read GAM files internally and no longer needs JSON preprocessing.
  • The vg giraffe minimizer file format has changed.
  • There is also a new .zipcodes index file used in vg giraffe mapping.
  • Improvements have been made to the distance index format used in vg giraffe.
• Haplotype information files used in haplotype sampling are a bit smaller. Existing files can still be used.
• Allow selecting the identity field in vg filter --tsv-out
• vg giraffe, vg mpmap, and vg map will now fail early with an error when encountering a read with a quality string of the wrong length (as from a truncated FASTQ)
• vg now tries to limit itself to a good number of threads for the number of CPUs in any enclosing Slurm job, via SLURM_JOB_CPUS_PER_NODE and CPU affinity masks.
• vg chunk can now properly take a chunk of a path that already has a subrange
• vg inject now has --add-identity to calculate 'identity' statistic (e.g. for linear mapper output BAMs)
• Add vg primers to get stats about variants in PCR primers from primer3
• Stop identity() from penalizing soft clips (insertions at start/end of path) as part of the total length
  • Note that this changes calculation used for the identity field in GAM files!
• vg autoindex will no longer duplicate input gbz as .giraffe.gbz when indexing for Giraffe.
• GAF sorting with vg gamsort is much faster than before.

Updated Submodules

The dozeu, gbwt, gbwtgraph, libbdsg, libhandlegraph, libvgio, and sublinear-Li-Stephens submodules have been updated.

vg 1.62.0 - Ranzano

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chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.62.0

Buildable Source Tarball: vg-v1.62.0.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:

• GBWT construction from a GAM/GAF file now uses parallel construction jobs.
• vg chunk and vg find now generate subpaths with subrange metadata when cutting up paths.
• vg gbwt will accept subranges on fragment 0 and discard the fragment number.
• vg map, vg mpmap, and vg giraffe can now annotate output with SAM-style flags from FASTQ comments with --comments-as-tags
• vg surject now detects when multipath alignments obviously don't belong to the graph they are being surjected to.
• Updated libbdsg to check if a distance index actually has distances and to improve memory use of distance indexing when not including distances
• vg index now includes include flag --no-nested-distance to build a distance index with distances only on the top-level chain
• Add --snarl-sample to vg stats -R. This adds BED-style reference coordinates to the front of each row in the snarl output table, using the input sample to select reference paths. If no selected path is found .'s are written. If multiple paths / intervals find (in case of cyclces), the first one found is printed.
• vg deconstruct -n bug that bypassed some nested sites fixed.
• When reading a .gff3 file with vg rna, validate exon ordering by base-pair position instead of number attribute. This allows reverse-strand exons to be numbered either by base-pair order or transcription order.
• Have vg rna gracefully ignore features with bad chromosome names if they're not included in --feature-type and thus won't be parsed anyways

Updated Submodules

The gbwt, gbwtgraph, gcsa2, libbdsg, libvgio, sdsl-lite, and sublinear-Li-Stephens submodules have been updated.

vg 1.61.0 - Plodio

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.61.0

Buildable Source Tarball: vg-v1.61.0.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:

• Changed the protocol of the elfutils submodule from git:// to https://
• Set snarl distance to 0 in path normalizer now that distance index is fixed.
• GCSA indexing now checks for I/O errors on temporary kmer files.
• make get-deps can no longer demand you set a timezone even when DEBIAN_FRONTEND=noninteractive in the calling shell.
• vg chunk can now reference-index particular haplotype paths when requested.
• vg paths -o added to apply a ReferencePathOverlayHelper before looking at the paths.
• Mac CI now uses macOS 15 base image.
• source_me.sh is no longer needed.
• fix validate bug on protobuf graphs
• vg surject --prune-low-cplx should no longer assess different contexts for different orientations of the same read, and should properly detect short tail anchors.
• sublinear-Li-Stephens now builds with the same compiler as the rest of the vg build
• vg rna can now output a haplotypes GBWT with node IDs matching the spliced graph

Updated Submodules

The libbdsg, sdsl-lite, and sublinear-Li-Stephens submodules have been updated.

The elfutils submodule URL has changed; make sure to git submodule sync.

vg 1.60.0 - Annicco

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chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.60.0

Buildable Source Tarball: vg-v1.60.0.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's self-reported version information should no longer be able to lag behind the actual Git revision checked out
• vg stats --snarl-contents added to print a table of snarl / depth / parent / nested node ids
• vg inject can now handle reads that softclip after the end of the target path
• vg paths -n option added to normalize graphs using path information to "snap together" redundant paths through snarls. After running, no two path traversals through a snarl will ever produce the same sequence string without the traversals themselves being identical.
• vg build system no longer patches kff-cpp-api CMakeLists.txt.

Updated Submodules

The kff-cpp-api, libbdsg and sublinear-Li-Stephens submodules have been updated.

vg 1.59.0 - Casatico

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chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.59.0

Buildable Source Tarball: vg-v1.59.0.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:

• Experimental haploid scoring model for haplotype sampling.
• Faster BAM output when using a GBZ format graph
• vg inject no longer reports invalid alignments
• vg giraffe --parameter-preset long-form option should now work again
• vg surject now complains if extra command line arguemnts are provided
• vg Mac builds no longer pass -headerpad without an argument to the linker
• vg giraffe in non-chaining single-end mode will again prioritize minimizers the same way as in paired-end mode
• README no longer interpretable as suggesting that users build with very old Clang
• vg surject now uses an unlimited --max-anchors by default
• vg clip faster on graphs with high path depth
• vg surject has improved base-level alignment accuracy with long reads
• Random walk band padding is now available outside MultipathAligner
• Gapless extension queue order should no longer cause vg giraffe output to very across compilers
• vg giraffe --show-work no longer claims to not be doing rescue when it is
• vg annotate can now output alignments in GAF.
• When reading more than 1000 BED or GFF records, vg will no longer dump the first records to standard output and forget about them.

Updated Submodules

The libbdsg and libhandlegraph submodules have been updated.

vg 1.58.0 - Cartari

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.58.0

Buildable Source Tarball: vg-v1.58.0.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 deconstruct now does path-based (formerly -e) deconstruction by default. Old default behaviour of exhaustively processing (tiny) sites is deprecated.
• if -a is not used, vg deconstruct will recursive on child snarls of snarls it failed to process (like vg call) - functionality that was, I think, dropped a while back.
• Experimental option -L added to vg deconstruct in order to cluster similar allele traversals together. The value given is a (length-weighted) threshold for the jaccard coefficient between the oriented nodes of two traversals. So if -L 0.75 is given, then alleles that have >= 0.75 similarity based on their graph positions will be merged into one. Two new FORMAT fields are added to keep track of the difference, TS (jaccard distance) and TL (length difference). Clustering is done greedily starting with selected reference paths.
• new (experimental) option -n added to vg deconstruct. Like -a, it genotypes nested sites, but unlike -a it does so top-down, setting various tags that keep track of the nesting relationship at the allele level (and also linking every site back to its position on the LV=0 reference chromosome). *-alleles (used in recent VCF versions to represent spanning alleles) are used. This option will not support nested insertions on GBZ/GBWT input -- so in practice it should be used on chromosome-level .vg files (I will look into relaxing this).
• -R option added to vg deconstruct to toggle whether star-alleles are reported with -n.
• README now explains how to get vg on your PATH
• README now explains how to build on multiple threads
• vg can now read GAM files generated by the long-read Giraffe prototype
• vg filter now lets you require exact matches for name filters instead of prefix matches with --exact-name.
• deconstruct/call can write giant VCF lines. This happens in, say, large svs with lots of samples that each get their own allele due to nested variation (hopefully deconstruct -L can mitigate this via merging). Giant AT fields for each allele don't help. bcf apparently has a 2 gig line limit, and there's a case of deconstruct seemingly truncating large records. vg deconstruct / call are now modified to drop (with a warning) any lines >2Gb to avoid these issues.
• vg giraffe should no longer crash when mapping paired-end reads and reporting secondaries without a fragment length distribution
• vg inject now supports GAF format with the new --output-format/-o option

Updated Submodules

• libvgio

vg 1.57.0 - Franchini

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.57.0

Buildable Source Tarball: vg-v1.57.0.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:

• Added haplotype sampling example
• Added subpath support to vg annotate
• Duplicate words removed from documentation
• WFAExtender alignments are now scored using the full length bonus
• Extra debug messages removed from vg chunk
• libdeflate build should now have more space to be renamed

Updated Submodules

None

vg 1.56.0 - Collalto

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.56.0

Buildable Source Tarball: vg-v1.56.0.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 GFA output should now use P lines instead of W lines when nonzero phase blocks are present, to allow them to be round-tripped.
• vg call -c and -C options changed to limit search based on all alleles and not just reference allele. This means these options work much better in practice to prevent vg call from being lost in giant snarls.
• --progress option added to vg call
• Paths with subranges on phase block 0 (or on haplotype paths without explicit phase blocks) can now be saved to GFA again.
• vg now supports reading from indexed GAF files of reads in many places where an indexed GAM file can be used

Updated Submodules

• htslib

vg 1.55.0 - Bernolda

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.55.0

Buildable Source Tarball: vg-v1.55.0.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 gamcompare now keeps track of whether reads could have possibly been gotten correct, based on there being a truth position for them in the truth set, and excludes reads without a truth from plots and accuracy statistics.
• vg giraffe no longer produces alignments with deletions on one end
• Multithreaded path cover / local haplotypes GBWT construction.
• CI should no longer fail due to truncated FTP download
• GBZ paper citation link now points to the right place
• vg surject will left align relative to the forward strand most of the time.

Updated Submodules

• gbwtgraph