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Published by adamnovak almost 5 years ago
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:
vg paths
can be used to remove paths from a graph.toil-vg
version in testing.vg gaffe
.vg gaffe
.libsdsl
build.vg depth
.vg pack
.vg augment
now cuts off softclips by default.vg explode
functionality now subsumed by vg chunk
.VGSet
object now supports HandleGraphs.make man
.vg call
.vg rna
.vg chunk -p
now contain offsets.Paths
object.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.The BBHash
, libbdsg
, libhandlegraph
, pinchesAndCacti
, and xg
submodules have been updated.
Make sure to git submodule update --init --recursive
if building from source.
Published by adamnovak almost 5 years ago
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:
vg gaffe
vg rna
vg call
bugfixes for cyclic graphsgiraffe-wrangler.sh
scriptvg mpmap
that should resolve some slowdownsvg rna
bugfixes for variants at the ends of exonsvg call
vg find
vg prune
vg call -b
parsing issue-s
option to vg augment
to ignore out-of-graph alignmentsvg pack
vg augment
vg index
now supports any graph filetype, not just .vg
.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.
Published by adamnovak about 5 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.19.0
Buildable Source Tarball: vg-v1.19.0.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:
The experimental vg mcmc
command, a Markov-chain-Monte-Carlo genotyper prototype
Improved clustering and intermediate scoring logic in vg gaffe
, and the elimination of MultipathAlignments from that pipeline
vg gaffe
now emits MAPQ 0 for unmapped reads
Handle-graph-ification of vg map
, phase unfolding, vg vectorize,
vg find,
vg chunk,
vg call`, and other operations using the xg index. Many commands now support more file types as arguments.
Phase unfolder path verification no longer runs in parallel
A new and improved XG index implementation. Note that backward compatibility is available only for XG indexes created with vg 1.18 or newer
Giraffe Wrangler script now counts only mapped reads for identity computation, can take its inputs from Amazon S3, and binds BWA to a single NUMA node
GBWT accesses now cached
Giraffe Facts now reports statistics by filter instead of by mapping stage
Vendored Protobuf submodule has been removed. vg
can now build with (and indeed now requires) system-installed Protobuf 3 from a package manager
vg call
algorithm has been revised to use the much more efficient "pack" format, allowing much larger single calling operations
A paired-end clustering algorithm for use in vg gaffe
has been added, but not yet used
Warnings about deprecated pointer types in lru_cache
eliminated
A new Dockerfile for a multi-stage build has been integrated directly into the vgteam/vg
repository. The vgteam/vg_docker
repository should no longer be required.
The GBWTGraph
has been moved to a submodule
Added a magic number system to identify bare XG files as XG files
Testing of builds of vg on Mac with GNU GCC has been discontinued. It is very difficult to get GNU GCC to build with the libc++ standard library, which packaged Protobuf builds for Mac use. GNU GCC should still work with Protobuf built with GNU GCC against its default libstdc++.
vg version
now reports the C++ standard library used in the build
CFLAGS and CXXFLAGS are now honored by submodule dependencies in more (but not all) places. Some dependencies still ignore them.
There is now a make static-docker
target which quickly builds a static vg
binary in the checked-out source tree and dumps it into a Docker container
The build system now has its own opinion about whether the current vg binary is statically linked, as recorded by a marker file in lib/
.
User support for vg
now ought to happen on Biostars: https://www.biostars.org/t/vg/
Crash bug in optimal_score_on_genome
has been fixed
Memory leaks in vg map
have been plugged
Protobuf 3.0 or greater, including libraries and compiler.
The protobuf
submodule has been removed.
The DYNAMIC
, gbwt
, gcsa2
, gfakluge
, libbdsg
, libhandlegraph
, libvgio
, lru_cache
, and sdsl-lite
submodules have been updated.
The gbwtgraph
, ips4o
, mmmultimap
, and xg
submodules have been added.
Make sure to git submodule update --init --recursive
if building from source.
Published by jeizenga about 5 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.18.0
Buildable Source Tarball: vg-v1.18.0.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
indexes. Must now use vg gbwt
.vg mod -g
now preserves embedded paths.vg call
and vg snarls
can now use any HandleGraph
implementation, which can significantly reduce memory usage.XG
files.gaffe
mapper through caching and altered alignment algorithms.GBWTGraphs
that can replace the XG
used gaffe
, significantly lowering memory usage.XG
to facilitate alternate backend data structures.vg gamcompare
.vg mpmap
.VG
graphs.vg deconstruct
.None
The FlameGraph
submodule has been added.
The sglib
submodule has been replaced by libbdsg
.
The libvgio
submodule has been updated.
Make sure to git submodule update --init --recursive
if building from source.
Published by Robin-Rounthwaite over 5 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.17.0
Buildable Source Tarball: vg-v1.17.0.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 annotate edited to search further for path hits.
Single-ended Dijkstra algorithm factored out into its own HandleGraph algorithm.
HandleGraphs can be loaded from files with dynamic implementation selection
Fixed bugs in minimum distance clustering
Fixed bugs in AlignmentEmitter
vg gaffe
improved speed and memory
GBWT manipulation tools in vg gbwt
vg mod -i
deprecated, replaced by vg augment -i
vg edit
mostly refactored into augment.cpp, except for the interface with lists of paths.
'vg find -E' extracts nodes with an id range defined by a path interval.
vg convert
allows graph type conversion between graph implementations.
vg gbwt
now considers unphased homozygous variants as phased to prevent phase breaks. This can be disabled with option -z
.
Improved vg compilation on MacOS with gcc 9
pack -q
allows weighting support by mapping quality.
Bug fixed in split strand overlay
Bug fixes with compilation errors using G++ 9.1.0.
Bug fix in tcmalloc.
Speed up vg filter
vg call
now supports pack graph format.
xg moved into vg namespace.
vg call
can now call sites in parallel.
Names added to transcripts written to the gbwt index. Transcript naming has been simplified.
gam output option from gbwt is removed. Gam files can be generated from gbwt transcript index using vg paths
.
Small speed-up for merging packer objects in vg pack
.
Options added for adding either reference paths or non-reference paths as embedded paths in a graph.
vg deconstruct
now works with more input graphs.
PackedGraph and HashGraph now moved to sglib.
vg paths -F
now writes embedded paths in FASTA format.
Factored out path-to-component index from XG
Bug fix in rewrite_segment.
Published by adamnovak over 5 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.16.0
Buildable Source Tarball: vg-v1.16.0.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 index
vg gbwt
vg call
GaplessExtension
support in the GaplessExtender
and in vg gaffe
vg gaffe
vg gaffe
heuristicsPackedGraph
PackedGraph
and HashGraph
vg rna
libvgio
.libvgio
.vg gaffe
performanceSnarlManager
vg chunk
vg call -f
vg snarls -m
vg gaffe
PackedGraph
storage backend with greater compressionMEMChainModel
vg map
None
The libvgio
submodule has been added.
The gbwt
, gcsa2
, libhandlegraph
, protobuf
, sonLib
, structures
, and vcflib
submodules have been updated.
Make sure to git submodule update --init --recursive
if building from source.
Published by adamnovak over 5 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.15.0
Buildable Source Tarball: vg-v1.15.0.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 rna
improvementsGBWTGraph
for "haplotype-consistent traversal"vg surject
BAMsvg::VG
move constructor that actually worksAlignerClient
base class for everything that uses Aligner
sAlignmentEmitter
.
ALTs in input VCFvg gaffe
None
The libhandlegraph
submodule has been added.
The fastahack
, gbwt
, and gssw
submodules have been updated.
Make sure to git submodule update --init --recursive
if building from source.
Published by jeizenga over 5 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.14.0
Buildable Source Tarball: vg-v1.14.0.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 minimizer
.vg surject
now performs forced full-length alignments by default instead of with a command line flag.vg surject
.vg call
on deletions.vg call
that caused crashes on some graph topologies.vg chunk
that would produce graph chunks that were inappropriate for variant calling.vg call
should call variants.vg index
.vg mpmap
on graphs with tight cycles.vg mpmap
's anchoring heuristics.vg filter
.vg msga
can be directed to align specific regions.vg validate
and vg mod
None
The structures
submodule has been updated. Make sure to git submodule update
to get it if building from source.
Published by adamnovak almost 6 years ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.13.0
Buildable Source Tarball: vg-v1.13.0.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 mod
to vg augment
None
The dozeu
and gbwt
submodules have been updated. Make sure to git submodule update
to get them if building from source.
Published by adamnovak almost 6 years ago
Published by adamnovak almost 6 years ago
Docker image: quay.io/vgteam/vg:v1.12.0
This release includes:
vg mpmap
vg construct
vg filter
to defray away entire readsVG::edit
vg simplify
vg call
without passing the base graphvg mpmap
None
The following submodules have been updated: vcflib
,
Published by jeizenga about 6 years ago
Docker image quay.io/vgteam/vg:v1.11.0-0-gea4aaded-t238-run
This release includes:
vg surject
to preserve long insertions or deletions.vg construct
.vg mpmap
.vg add
.vg index
for computing distances.clang
compilation.vg construct
that led to invalid GBWT indexes.make clean
's cleaning of some dependencies.vg genotype
on low-coverage samples.None
The following submodules have been updated: gfakluge
, vcflib
, gbwt
, and gcsa2
.
Published by adamnovak about 6 years ago
Docker image: quay.io/vgteam/vg:v1.10.0-0-ga4811915-t226-run
This release includes:
.vg
and .gam
, are now blocked-gzip compressed to permit random access.vg gamsort
) for efficient random access to reads in GAM files.vg mpmap
aligner and its MAPQ computation.vg paths
so paths extracted from a GBWT are now valid.vg paths
.vg augment
interface.vg snarls --max_nodes
.xg::XG
public interface.vg find
no longer has a -i
/--alns-in
option. You should use --alns-on
instead; it's much simpler to think about.vg msga
behavior has changed.None
The vcflib
and htslib
submodules have been updated.
The dozeu
and libdeflate
submodules are new.
The htslib
submodule has moved to https://github.com/vgteam/htslib. Developers will need to do a git submodule sync
.
Published by adamnovak over 6 years ago
Docker image: quay.io/vgteam/vg:v1.9.0-0-g3286e131-t206-run
This release includes:
vg deconstruct
(as the command is still under development)vg construct -S
)vg filter -d
vg version
vg version
output looks different. Anyone who may be parsing it will need to adapt their code.None
The fastahack
, gbwt
, gcsa2
, gfakluge
, and vcflib
submodules have all been updated.
The fastahack
submodule has also moved to https://github.com/vgteam/fastahack. Developers will need to do a git submodule sync
.
Published by adamnovak over 6 years ago
Docker image: quay.io/vgteam/vg:v1.8.0-0-g3cb239e2-t176-run
This release includes:
vg viz
native graph rendering toolNow vg depends on Cairo, which vg viz
uses for drawing.
The gbwt
and raptor
submodules have been updated.
Published by ekg over 6 years ago
This release roughly coincides with resubmission of the vg paper. There have been a lot of changes since v1.6.0 and it would be difficult to provide a specific summary, but several items deserve mention.
Published by ekg almost 7 years ago
This checkpoints the version that was used to generate experimental results in the preprint of our manuscript. (It will be linked here when made public.)
Attached is a stripped static binary that is portable across all 64-bit Linux systems that we have access to.
Published by ekg over 7 years ago
Recent developments in vg have focused on improving the mapper's performance via simulations.
As a result of this work, our simulations show that when aligning reads simulated from the 1000G variation graph, vg
is equivalent to bwa mem
in performance on the linear reference, and bests it considerably when aligning against the pangenome:
Experiments are completed with scripts/map-sim
. The above example can be reproduced by:
vg/scripts/map-sim human.10M hs37d5.fa ref/index pan/index 32 "-s 571 -n 500000 -e 0.01 -i 0.002 -l 150 -p 500 -v 50" " "
Runtime is between 5 and 10x that of bwa mem
.
Published by ekg over 8 years ago
There have been 286 commits since v1.3.0, so it is hard to summarize everything that's happened. Here are some of the highlights:
Published by ekg almost 9 years ago
Since v1.2.0:
The changes in format necessitated changes in xg, and any indexes from older versions will be invalidated with this update.