vg 1.33.0 - Moscona

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.33.0

Buildable Source Tarball: vg-v1.33.0.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 call -a fixed to not include redundant base at beginning of alleles
• "path end" field corrected in GAF output
• VG now supports ARM Macs.
• vg recalibrate has been removed (deprecated since 1.30.0).
• vg find kmer output also lists samples/phases for the matching haplotypes.
• vg's GAF parser now reads cg cigar strings when no cs cigars found so, for example, vg pack can now properly load a GAF from GraphAligner.
• vg gbwt -R now removes multiple samples correctly.
• vg deconstruct can more easily use reference paths (or subpaths) from the GBWT
• vg mcmc now accepts non-vg::VG graphs as input
• vg deconstruct fixed to not write sites with no alt alleles when genotyping with a gbwt

New and Updated Submodules

The DYNAMIC, gbwt, gbwtgraph, gcsa2, libhandlegraph, libvgio, and vcflibsubmodules have been updated. Thehtslibandtabixppsubmodules have been added. Thevowpal_wabbit` submodule has been removed.

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

vg 1.32.0 - Sedlo

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.32.0

Buildable Source Tarball: vg-v1.32.0.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 tests with sequenceTubeMap
• vg map and vg mpmap now annotate properly-paired read mappings
• vg stats -a reports proper pairing statistics
• Faster graph to GFA conversion with vg convert.
• vg surject now gives a helpful warning if you try to use an unsurjectable GAF, rather than just crashing
• GBWT index can now be used to find alt alleles in vg deconstruct with -g
• Single nodes at the end of bridge paths in the Cactus graph won't show up twice in the snarl decomposition
• Giraffe self-profiling is improved and a standardized speed test script is included
• vg construct can accept multiple --region arguments for different contigs
• Convert GBWTGraph to GFA with vg convert.
• VCF files with * alleles are now accepted by vg construct, and only the particular variant records with * alleles are rejected and warned about
• Uncompressed GFA files can now be directly input (or streamed via stdin) as graphs into vg commands. (previously vg convert -g was required beforehand)
• Karger-stein min cut alogirtm and alt proposal distribution added to vg mcmc genotyper. Scripts for performance analysis are in scripts/MCMC_makefile.sh, scripts/mcmc_dist.sh.
• Count the number of nodes with self-loops with vg stats.
• vg srpe has been removed
• vg mod options --kill-labels and --strong-connect have been removed.
• vg stats -L counts self-loops.
• vg stats -e lists nondeterministic edge sets.
• vg find option --mapping enables finding nodes that map to the selected ids.
• vg is now able to build bundled htslib on Autoconf 2.70+

New and Updated Submodules

The fermi-lite, gbwt, gbwtgraph, 'gcsa2', gfakluge, jemalloc, libvgio, and sdsl-lite submodules have been updated.

Make sure to git submodule sync and git submodule update --init --recursive if building from source. The jemalloc update is also known to not build over top of a previous built version; you may need to rm -Rf deps/jemalloc and git submodule update --init --recursive to fix it in your copy.

vg 1.31.0 - Caffaraccia

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.31.0

Buildable Source Tarball: vg-v1.31.0.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:

• Large variants are now always handled as flat, and not aligned to themselves, in vg construct.
• rGFA files (such as those output by minigraph) can now be imported into vg with vg convert -g
• vg autoindex can now construct indexes for the vg mpmap/rpvg transcriptomic pipeline and the vg giraffe tool
• Cigar overlaps replaced with *'s and trailing tabs removed to make GFA output more compliant with 1.0 spec.
• GBWT and GBWTGraph construction from GFA input.
• vg convert can convert GBWTGraph to other graph formats.
• Fixed typo in the IntegratedSnarlFinder test case description
• XG indexes now take somewhat less space (especially those with many paths).
• vg convert can output vg paths (that adhere to certain naming conventions) to GFA W-lines with the -w option.
• Build should fail less on GCC 10.2.1-1.
• vg convert can now output GFA, with selected reference paths written to "rank 0" rGFA tags
• vg combine no longer loads graphs as, and writes graph to, protobuf. Also fixed to join id spaces if necessary.
• vg now uses the vgteam fork of SDSL.
• CI now moved to Gitlab and Github Actions.
• vg autoindex can now simplify plans with joint recipes
• IndexRegistry uses per-instance temp directories
• vg Docker build is now optimized for layer caching
• vg can now build on the arm64 architecture and pass unit (but not CLI) tests
• Updated to latest vgteam version of the DYNAMIC library
• Converting GFA with P-lines and W-lines into GBWTGraph stores the P-lines under sample name _gbwt_ref.
• vg convert from GBWTGraph to another graph type stores the threads for a specified sample (default _gbwt_ref) as paths.

New and Updated Submodules

• DYNAMIC, fermi-lite, GBWT, GBWTGraph, GCSA2, gssw, libbdsg, mmmultimap, sdsl-lite, ssw, and xg have been updated.
• mio and atomic_queue have been added.

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

vg 1.30.0 - Carentino

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.30.0

Buildable Source Tarball: vg-v1.30.0.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 paths now has -C option to list which paths are cyclic and which aren't
• fixed vg view bug which caused outputting to GFA to use too much memory
• Giraffe can now --show-work to explain itself.
• Giraffe funnel plots no longer invent fake candidates
• Giraffe now maps and caps MAPQs properly with syncmers
• vg mpmap produces more complete multipath alignments around indels in low complexity sequences.
• Update libvgio dependency (fixed cmake handlegraph dependency)
• The following subcommands are now deprecated: combine, compare, explode, join, kmers, locify, msga, recalibrate, sift, sort, srpe, translate.
• The following subcommands have been deleted: bugs, crash.
• Crash reports now direct users directly to the new issue URL
• rocksdb is no longer a dependency.
• vg index no longer will produce RocksDB indexes of GAMs or graphs.
• vg find can no longer be used to query from RocksDB indexes.
• vg genotype no longer accepts RocksDB GAM indexes, and instead accepts only GAMs.
• vg gamsort can no longer sort using the RocksDB order.
• vg compare has been removed.
• vg locify has been removed.
• The following subcommands are now deprecated: concat, explode, join, kmers, msga, recalibrate, sift, sort, srpe, translate.
• vg prune is now more memory efficient.
• Giraffe mapping quality cap is now more numerically stable and fails assertions less
• The roc plot script now runs

New and Updated Submodules

A submodule for the wiki has been added in doc/wiki.

Thelibbdsg, libhandlegraph, and libvgio submodules have been updated.

The rocksdb submodule has been removed.

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

vg 1.29.0 - Sospiro

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.29.0

Buildable Source Tarball: vg-v1.29.0.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:

• XG indexing now uses the temporary directory also for SDSL temp files.
• New GBWT construction interface in vg gbwt.
• vg mpmap now can perform multiple spliced alignments on one read and spliced alignments on multiple mappings.
• Update to latest vcflib ("Configure for default, libcurl-using HTSLib config") to get non-x86 support
• Cross building for other architectures is now easier due to the use of $PKG_CONFIG for specifying pkg-config binary
• SAM/BAM/CRAM TLENs should now match BWA's for identical alignments
• Remove multiple samples with vg gbwt -R.
• Mac builds on Catalina no longer fail with a "missing separator" error.
• CIGAR strings in SAM/BAM/CRAM should now consistently coalesce runs of adjacent insertions and deletions.
• Readme no longer encourages using the unsupported GNU GCC build on Mac.
• Spliced multipath alignments are strand consistent and have a more complete representation of variation near splice sites.
• vg filter can now work on GAMP files with -M, and reads with a given subsequence can be filtered with -a and -A.
• vg mod -n should now work properly when self loops happen at the ends of merged nodes
• CIGAR strings for spliced surjection from GAM files now have correct intron lengths
• CI now tests macOS 10.15
• vg now uses (and needs!) system Boost for Vowpal Wabbit instead of bundling a subset
• Parallel GBWT merging algorithm in vg gbwt.

New and Updated Submodules

The gbwt, mmmultimap, vcflib, vowpal_wabbit, and xg submodules have been updated.

The source repository for the vowpal_wabbit submodule has moved.

The boost-subset submodule has been removed.

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

New dependencies

Instead of shipping a subset of Boost, vg now requires Boost to be installed on the system already in order to build.

vg v1.28.0 - Acquafredda

Changes in this release:

• vg surject now supports GAF input with -G.
• vg surject can now take GAMP files from vg mpmap as input with -m
• vg surject is now substantially faster
• vg mpmap can now toggle between output formats (including single path and linear formats) with a single option. Some command line arguments have changed semantic meaning.
• vg mpmap's spliced alignment is now significantly more accurate.
• Divided handles with reversing self-edges no longer drop the edge.
• New path cover GBWT defaults: n = 64 for local haplotypes and 16 otherwise.
• Giraffe now properly sets paired end read cross-references
• vg deconstruct includes new option -a to process every snarl (instead of just top-level snarls)
• vg mpmap -m now correctly removes the full length bonus from reported scores
• -lpthread and -lm can be linked dynamically again
• Base quality-adjusted scoring now adjusts the full length bonus.
• Updated with less-patched Raptor dependency
• vg convert calls with -g as the last option will now convert to the correct format, not always Protobuf
• Now vg outputs raw handle graph files readable by libbdsg without the need for vg view -x/--extract-tag.
• vg msga handles terrible alignments better.
• vg giraffe can now output to SAM/BAM/CRAM directly
• Dependency retrieval no longer upgrades already-installed packages
• vg giraffe, vg map, vg mpmap, and vg surject now take a .dict file to order HTSlib sequence headers via --ref-paths.
• GaplessExtender no longer matches non-ACGT characters.
• SAM header lines in dict files are now tested
• vg add now supports overlapping reference paths, as in Cactus graphs

New and Updated Submodules

• libvgio, raptor, dozeu, and vcflib have been updated.
• htslib has been removed. We now use the HTSlib from vcflib.

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.