vg 1.27.1 - Deliceto

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.27.1

Buildable Source Tarball: vg-v1.27.1.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:

• No longer crashes when converting GFAs that lack a header line
• GAF support in vg paths
• GAF support in vg augment
• vg mpmap can now produce spliced alignments when using the rna preset
• vg gampcompare now handles spliced GAMP files correctly
• Build an r-index with vg gbwt.
• vg snarls -e will output a traversal for every embedded path through each snarl, regardless of snarl complexity
• Refactored vg gbwt.
• Fixed a rare GaplessExtender bug.
• Use the same temp directory for all submodules in vg index.
• Faster parallel GAF input streaming, especially in vg pack.

New and Updated Submodules

The gbwt, gfakluge, and libvgio submodules have been updated.

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

vg 1.27.0 Deliceto

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.27.0

Buildable Source Tarball: vg-v1.27.0.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:

• mpmap's agglomerate option fixed for paired-end reads

vg 1.26.1 - Stornara

This is a patch release intended to serve as a the version of vg for the paper on the vg giraffe mapper.

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.26.1

Buildable Source Tarball: vg-v1.26.1.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:

• Multipath alignments have correct copy and move operators
• vg annotate -m can annotate reads with a path position for each Mapping to a node
• vg annotate now actually respects passed search limit (-l)
• Align promising partial extensions in Giraffe.
• gampcompare now returns the correct distances with the -d option
• vg mpmap -a now agglomerates multipath alignments into a single disconnected alignment (-a no longer controls the maximum alignments through a snarl)
• mpmaps MAPQ now incorporates multiplicities from cluster and alignment hard caps
• vg depth now supports GAF input
• "no sequence" mode using vg view -du where the node sequence is replaced by its size, e.g. to visualize large graphs with dot
• vg sim -E now produces correct positions in single-end simulations
• vg gampcompare output now includes a column to indicate if a read was mapped
• vg surject -S no longer produces occasional malformed BAM records
• Improved heuristic for choosing the extensions to align in Giraffe.
• New option -a for vg call includes 0/0 calls. It can help compare and merge VCFs from multiple samples called against the same graph.
• vg mpmap -a no longer crashes on read pairs that fail to find a consistent pair of mappings
• Update giraffe mapping quality caps

New and Updated Submodules

The raptor submodule has been updated.

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

v1.26.0 - Stornara

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.26.0

Buildable Source Tarball: vg-v1.26.0.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 gbwt -a adds a path cover of components without haplotypes to an existing GBWT. This resolves the Giraffe issue with a large number of incorrect mapq 60 reads in some graphs with the full GBWT.
• New seeding algorithm targeted at miRNA
• More flexible build system
• Pangenome ontology now has linkZoomLayer
• Synchronized semantics for OVERLAP_THRESHOLD
• Chopping with mod -X changed to run natively on handle graphs
• vg stats -F prints graph format
• Major vg index refactor.
• Always build GBWT from a single graph with a single thread source (VCF, GAM, GAF, paths).
• Index embedded paths as samples instead of contigs with vg index option --paths-as-samples.
• Correct names for long options in vg gbwt.
• Ignore metadata in empty indexes when merging GBWTs.
• add vg stats -D option to print degree distribution
• GAM/GAF I/O code moved into libvgio
• Ability to specify contig ploidy in vg sim
• Alignment with dozeu can now handle large full length bonuses without crashing
• dozeu is now non-x86 compatible.
• Made match pruning in mpmap less aggressive for very short reads
• mpmap can now use the distance index's algorithm for rescue graph extraction
• mpmap now can use the distance index in place of a snarl manager to guide the structure of multipath alignments
• Better vg map error message when xg input not found
• GBWT construction from GAM/GAF is faster and handles duplicate read names correctly.
• vg sim can now output a table of the path positions that reads were simulated from
• Added a subcommand gampcompare to evaluate mapping correctness of multipath alignments
• libvgio now only tries to find Protobuf once
• Memory should no longer blow up in mpmap on splice-abundant graphs
• GaplessExtender returns all non-overlapping full-length extensions.

New and Updated Submodules

The gssw submodule is pointing at a different repository. Use git submodule sync to update the pointer if building from source.

The libvgio, dozeu, gbwt, libbdsg, gssw, structures, and gbwtgraph submodules have been updated.

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

vg 1.25.0 - Apice

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.25.0

Buildable Source Tarball: vg-v1.25.0.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:

• New development in vg mcmc
• Graph Alignment Format (GAF) output support for vg map and vg giraffe
• Revisions to distance index format; distance indexes will need to be rebuilt
• STL-based multipath alignment internal format
• Bugfixes to Integrated Snarl Finder
• Improvements to dozeu alignment algorithm
• Bugfixes in banded global aligner algorithm
• CI tests rearranged into batches
• Bugfix for slow clustering in vg giraffe
• Parallel snarl finder in vg deconstruct
• Bugfixes to NetGraph in the absence of unary snarls
• Update to XG encoding
• Transfer mapqs when converting multipath alignments
• Bigger bins for coverage stats in vg call
• Better write parallelism in mpmap
• Case insensitivity for some mapper option values
• Fix build of SNarlManager with latest Protobuf which prohibits inheriting from messages
• Find the missing start indexes on multipath alignments
• New default gbwt id interval value in vg rna
• Renamed vg gaffe to vg giraffe
• Avoid out-of-bounds CNV and inversion breakpoints when generating random test graphs
• Bugfixes to variant caller
• Disqualify ultrabubbles with tips
• Fix vg rna crash when using reverse embedded paths
• Improvements to vg sim read simulation, especially for microRNA
• Don't enter infinite loop in vg sim when simulating from short paths
• Reduce information copying on multipath alignments
• Changed default vg giraffe parameters and added a fast mode
• Fix incorrect assert in vg sim
• Fix presets in vg mpmap
• Made clustering distance limit adjust itself for longer read lengths for vg giraffe
• Fix missing metadata for multipath alignments
• Added vg call option to output traversals to gentoype with rpvg
• Update CI to latest toil-vg
• Better Giraffe rescue
• Ploidy option for vg deconstruct
• Fix annotation boundary bug in vg rna
• Added -T option in vg call to pad traversals
• Added overlap threshold in GaplessExtender to deduplicate nearly identical vg giraffe results
• New seeding algorithm in vg mpmap targeted at miRNA

New and Updated Submodules

The gbwtgraph and xg, submodules have been updated.

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

vg 1.24.0 - Montieri

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.24.0

Buildable Source Tarball: vg-v1.24.0.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:

• Bugfixes in vg mpmap
• MEM finding heuristic in vg mpmap
• Pointers to Gimbricate and Seqwish when trying to import a non-blunt GFA
• A new IntegratedSnarlFinder that can be faster and use less memory, accessible through vg snarls --algorithm integrated
• Use of dozeu library for vg gaffe rescue
• Faster default mapping parameters in vg rna
• Fix for excessive memory use bug in spliced vg surject
• Fix for an off-by-one error in vg annotate gff parser
• Fix for getting seed distances from distance index
• Additional spliced vg surject bugfixes
• Added option to prespecify topological order for dozeu
• Top level clustering improvements for vg gaffe
• vg add can now work with various graph formats as input
• Made banded alignment traceback not recursive
• Minor optimizations in vg gaffe
• Added GBWT traversals option for vg call
• Shook more bugs out of mpmap presets and alignment
• Added a GBWT traversal finder
• Improved Turtle Pangenome Ontology
• Adjusted FTP URL where CI testing looks for its GIAB test data
• More use of dozeu in vg mpmap
• Support for quality-adjusted alignment in dozeu
• Revised vg mpmap CLI for better usability
• Added a no clustering option to vg mpmap
• Registered magic numbers for libbdsg graph types so they can be loaded without VPKG encapsulation
• Added node qualities to vg pack output format
• Updated internal dozeu and X-drop alignment interface
• Added ability to simulate from a specific sample in vg sim
• Update handle graph API to include node ranks
• Changed XdropAligner usage to be one per thread.
• Removed support for reading GFAs with overlaps: please preprocess with Seqwish to squash the overlaps out
• Cap the number of threads used in the Docker build to a reasonable number for Quay potatoes
• Automask IUPAC codes to Ns in vg construct, because the internal data model can't use them. If you want them in the graph, make them into variants.
• Chunk long paths when extracting paths Protobuf with vg paths
• Bugfixes to the ODGI graph implementation
• Boosted timeout for simulated chr21 CI mapping test
• Tweaked error rates used for vg call
• Substantial bugfixes in the FlowCaller
• Prohibit empty nodes in xg graphs
• Support for ODGI format in vg convert and as an input format more generally
• Added libbdsg, xg, and vg's algorithms and io namespaces to vg Doxygen docs
• Fixed excessive recursion when dealing with snarls
• Added MAPQ support for paired-end vg gaffe.
• Added ability to convert GFA files to other graph formats in vg convert

New and Updated Submodules

The dozeu, gbwt, gbwtgraph, gfakluge, gssw, libbdsg, libhandlegraph, pinchesAndCacti, structures, and xg submodules have been updated.

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

vg 1.23.0 - Lavello

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.23.0

Buildable Source Tarball: vg-v1.23.0.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 construct now rejects not-yet-implemented * allele from new VCF spec
• vg CI now runs on Kubernetes
• vg Docker can now be built with Kaniko
• vg gaffe now has MAPQ capping logic to reduce the error rate at MAPQ 60
• Default MAPQ settings in vg mpmap have been changed
• vg CI tests now respect the core limit of the container they are running in, instead of trying to use all the host's cores
• A variety of vg mpmap options were removed. Some short options changed their meanings.
• Mapping real RNA data with vg mpmap is now faster
• vg CI tests now use an updated toil-vg
• vg circularize adds graph edges once again when circularizing paths
• vg gaffe is now faster
• vg mpmap MAPQs are no longer miscomputed in rare cases
• vg gaffe's index finding has been completely redone. It can now create its own indexes or find indexes by prefix. This may lead to it picking up and using indexes that were not passed to it directly.
• Surjection of softclips has been improved.
• vg call now uses a better, flow-based traversal finding algorithm to generate alleles
• vg mpmap uses new algorithms for long-read alignment
• vg CI reports are no longer totally empty for some tests
• The internal XdropAligner is now much simpler
• ProtoHandleGraph is no longer needed and has been removed
• vg concat now works via the HandleGraph API, and has a -p option be path-guided
• HashGraph no longer crashes when incrementing node IDs
• Machinery for haplotype-based rescue in vg gaffe has been added
• XdropAligner now automatically finds the best pinning location

New and Updated Submodules

The gbwtgraph and libbdsg submodules have been updated.

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

vg 1.22.0 - Rotella

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.

vg 1.21.0 - Fanano

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.21.0

Buildable Source Tarball: vg-v1.21.0.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:

• Changes to how vg paths can be used to remove paths from a graph.
• Use of a new toil-vg version in testing.
• Changes to minimizer seed handling algorithms in vg gaffe.
• Some paired-end clustering logic to be used in vg gaffe.
• Improvements to the build system around the libsdsl build.
• No-hit read counting and better S3 support in Giraffe Wrangler script.
• A new subcommand, vg depth.
• Refactoring and race condition removal in vg pack.
• Probabilistic calling support.
• Improvements to snarl traversal enumeration.
• Improved ability of the build system to handle switching compilers.
• Bugfixes to the vg RDF ontology.
• vg augment now cuts off softclips by default.
• vg explode functionality now subsumed by vg chunk.
• Internal VGSet object now supports HandleGraphs.
• Some manpages available via make man.
• Better handling of reverse-strand cycles in vg call.
• Better gtf/gff parsing in vg rna.
• Snarl computation now parallel.
• Subpaths output by vg chunk -p now contain offsets.
• Fix a race condition when reading from the Paths object.
• Ability to chunk non-indexed GAM files by graph component.
• Bugfixes to kmer enumeration.
• Deprecated some vg mod flags, with warning messages.
• vg find can produce more information about kmers.
• vg construct should no longer drop the end breakpoints of deletions.

New and Updated Submodules

The BBHash, libbdsg, libhandlegraph, pinchesAndCacti, and xg submodules have been updated.

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

vg 1.20.0 - Ginestra

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.20.0

Buildable Source Tarball: vg-v1.20.0.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:

• Faster and more efficient minimizer finding and clustering in vg gaffe
• Memory usage optimizations in vg rna
• vg call bugfixes for cyclic graphs
• Improved giraffe-wrangler.sh script
• Improvements to tail anchor synthesis in vg mpmap that should resolve some slowdowns
• vg rna bugfixes for variants at the ends of exons
• Better use of overlays in vg call
• BED-based extraction in vg find
• High-degree node removal in vg prune
• Bugfix for vg call -b parsing issue
• New -s option to vg augment to ignore out-of-graph alignments
• Binaries and Dockers now built for Nehalem architecture and above; AVX1 instruction support should no longer be required
• Faster packing with vg pack
• Ability to build a GBWT from sampled local haplotypes rather than a whole haplotype database
• Coverage threshold for faster vg augment
• Distance indexing with vg index now supports any graph filetype, not just .vg.

New and Updated Submodules

The BBHash submodule has been added.

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

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