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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 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
htslib
Published by jeizenga 8 months ago
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 surject
will left align relative to the forward strand most of the time.gbwtgraph
Published by xchang1 9 months ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.54.0
Buildable Source Tarball: vg-v1.54.0.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 giraffe
now does diploid sampling.sample#contig
correctly.Published by adamnovak 11 months ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.53.0
Buildable Source Tarball: vg-v1.53.0.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 sim
no longer crashes on graphs with 1-node cyclesvg autoindex
can identify haplotypes specified as P-lines in a GFAvg gbwt
option --set-reference
.vg rna
no longer projects transcripts twice onto a reference given by RS
tag in a GFAvg rna
assigns unique names to twice-projected transcripts on cyclic haplotypesvg haplotypes
, the default number of candidates for diploid sampling is now 32.vg giraffe
now explains that --named-coordinates
works for GAF outputlibvgio
now uses quoted includes internallyvg
in your workdozeu
submodule should no longer crash vg giraffe
and vg surject
.dozeu
gbwt
libhandlegraph
libvgio
Published by jeizenga 12 months ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.52.0
Buildable Source Tarball: vg-v1.52.0.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 has a -A, --alt-paths-plain
option for storing IDs from the VCF instead of hash-based IDs for alt allele paths.vg call
patched so that certain problem cases no longer take forever.GRCh38#chr1
, with no haplotype phase number.diff
.vg haplotypes
.-O
help for vg call
CXX_STANDARD
variable in. You should be able to e.g. make CXX_STANDARD=20
if you have a Protobuf/Abseil for C++20.vg autoindex
rewinds to pruning if memory is too highPublished by adamnovak about 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.51.0
Buildable Source Tarball: vg-v1.51.0.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 giraffe
command line help; full list of options is still available with -h
.vg validate
now complains about duplicate path namesvg convert
option --no-translation
for converting GBWTGraph to GFA directly without using the node-to-segment translation.vg rna
will not crash when adding transcripts with an intron of length 0vg paths
now supports -H
for selecting haplotype paths and -R
for selecting reference pathsPublished by adamnovak about 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.50.1
Buildable Source Tarball: vg-v1.50.1.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:
vg autoindex --workflow map
can index GFAs with many W linesvg autoindex -w map
and -w mpmap
won't enter an infinite loop when they can't write to diskGRCh38#chr1
style path names in GFA P lines should now be parseable againgcsa2
libhandlegraph
Published by glennhickey about 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.50.0
Buildable Source Tarball: vg-v1.50.0.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
requires a distance index for building a minimizer index.-S
option added to vg call
to select reference paths by sample name. This is more convenient as it allows, ex -S GRCh38
to be used in place of -p GRCh38#0#chr1 -p GRCh38#0#chr2 ..
. Such selection is necessary when the graph has more than one reference sample and vg call
will now refuse to handle graphs with multiple reference samples unless paths are selected with -S
or -p
.vg filter
can filter to only mapped or only unmapped readsvg deconstruct
changed back to writing the full sample / hap/ contig name in VCF contig field. In order to just write the contig name (like in the past few versions of vg), use the new -C
option.gbwtgraph
gcsa2
libhandlegraph
libvgio
Published by adamnovak over 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.49.0
Buildable Source Tarball: vg-v1.49.0.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
can read BAM files with unmapped readsvg giraffe
now has --match
, --mismatch
, --gap-open
, --gap-extend
, and --full-l-bonus
options to control alignment scoring.vg deconstruct
on PGGB graph that was introduced in v1.48.0:
character now allowed in path name during contig:start-end
range extraction from command line options (ie in vg chunk
).vg clip
crash on PackedGraphs fixed.vg giraffe -b fast
preset now works again and is under testgbwtgraph
libbdsg
libvgio
Published by jeizenga over 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.48.0
Buildable Source Tarball: vg-v1.48.0.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 chunk
will now report an error if asked to chunk reads that do not go with the graphvg autoindex
can construct linear reference indexes from a FASTA filevg gbwt
will now refuse to add reference sample names with #
in them, and will try and advise on what the tags are supposed to be likevg surject
can project to paths that intersect themselves in the reverse orientationvg surject
will now print warning messages when processing a read or pair takes a suspiciously long amount of time.vg giraffe
should no longer try to put hypothetical sequencing errors in empty intervals, and should report errors in MAPQ cap computation in a more debuggable way.VG_FULL_TRACEBACK=0
to suppress it to a file.vg surject
and vg giraffe
should now include relevant read name hints when crashing in many cases.crash_unless()
as an alternative to assert()
that reports these hints. We eventually want to use it everywhere.vg surject
will limit itself to 200 anchors per target path segment by default; use the new -a/--max-anchors
option to control this limit. Surjection against PGGB graphs may require --max-anchors 20
to complete.vg surject
may be able to limit itself to considering only high-scoring surjections in some cases.vg construct
now properly handles the case where it is looking for the end of an inversion from 1 base before itvg construct
will no longer try and coalesce nodes at construction chunk boundaries when those nodes have alt paths that visit them or edges to their outside endpoints. This should fix some crashes and incorrect placement of structural variant breakpoints in the graph.vg construct
should now be faster when variants are extremely long and overlap each othervg chunk
now outputs PackedGraph instead of Protobuf by default (unless -T
is used). Also, output files now get the .vg
file extension for any non-GFA format (use vg stats -F
to check the underlying format of any graph).vg clip
fixed so that when there are multiple different reference traversals in a snarl (common in PGGB output), then none of them are chopped./usr/bin/time
for profilinghtslib
vcflib
gbwtgraph
libbdsg
tabixpp
Published by adamnovak over 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.47.0
Buildable Source Tarball: vg-v1.47.0.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 sim
and vg stats -a
sped up for GBZ inputvg construct
should no longer fail assertions and will instead report errors.vg construct
now handles IUPAC codes in the reference as Ns even if they are covered by symbolic structural variantsvg haplotypes
.vg stats -a
also outputs statistics on alignment scores and mapping quality.vg giraffe
should no longer crash if the distance index is read-only.vg rna
now supports the GBZ format for the input graph and haplotypes (new option --gbz-format
).vg convert
now defaults to PackedGraph instead of HashGraph if no output format selected.vg clip -s
to remove stubs (dangling nodes not on ref path)vg call
and vg deconstruct
now only apply node ID translation from GBZ inputs if new -O
is used.vg surject
will now enforce that the reads it is surjection actually were mapped against the graph you are surjecting against. Right now it checks node IDs and lengths. You can turn this off with -V
/--no-validate
.vg gbwt
now accepts a -I
/--gg-in
option, which lets you load a .gg
file and a .gbwt
file and combine them into a .gbz
graph.vg validate
now accepts a -A
/--gam-only
option which will validate only the provided alignment's agreement with the graph, and not the graph itself.vg surject
/vg giraffe
error: couldn't identify a path corresponding to surjected read
error message has been improved to dump more information about the offending read and path.[]
-enclosed subrange at the end. The base path name without the []
subrange coordinates should usually be used instead, because that is the space in which the SAM/BAM output will have its coordinates specified.vg surject
Graph does not have a path named
error message should now no longer print pointer values, and is extended to explain a bit more about subpaths.The kff-cpp-api
and libbdsg
submodules have been updated.
Published by xchang1 over 1 year ago
Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.46.0
Buildable Source Tarball: vg-v1.46.0.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 stats
now reports on time-usage information in GAM files if availablelibbdsg
and gbwtgraph
is now under CI test.vg giraffe
paired-end mode should no longer decide it rescued off of the wrong alignmentsvg inject
) will now bail out and complain if they are against haplotypes and not reference or generic paths (because positional lookup is likely to be too slow to be practical)vg inject
now defaults to the normal default number of threadsvg gamcompare
now has a -n
/--rename
options for comparing GAM files annotated with position on the same contigs but with different names.vg annotate
now uses a ReferencePathOverlayHelper to make sure it has fast access to the positions of graph nodes along paths.vg rna
will no longer in certain cases skip the first line when the annotation input has a headervg rna
no longer crashes when adding splice-junction from a BED file with intronsscripts/make_pbsim_reads.sh
now works with local graph files in addition to S3 URLsscripts/lr_benchmark.sh
now downloads and uses CHM13 graphsvg clip
edge clippingvg chunk
on GBZ inputvg haplotypes
subcommand for sampling haplotypes based on kmer counts.vg giraffe
now preloads the distance index into memory before mapping any readsprotoc
not being installedThe libbdsg
and gbwtgraph
submodules have been updated.
The kff-cpp-api
submodule has been added.
Published by adamnovak almost 2 years ago
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 nodesvg paths -C
reports both undirected (visit any node twice) and directed (visit any node twice in same orientation) cyclicityg++ --version
doesn't actually have the version string on the first lineodgi
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.stats -p
optionvg 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.vg mpmap
has increased sensitivity for detecting splice junctionsvg autoindex
can produce graphs (included spliced graphs) from FASTAs without requiring VCFsvg 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 filevg chunk
can use --no-embedded-haplotypes
to ignore haplotypes from a GBZ.The libbdsg
and libhandlegraph
submodules have been updated.
Published by adamnovak almost 2 years ago
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:
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.--num-bp-per-min
to Giraffe to adjust the number of selected minimizers based on the read length.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 tovg surject
has improved stability on cyclic graphsvg 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 rna
now support reference transcript paths where exon boundaries are on opposite strandsvg convert --drop-haplotypes
will drop haplotype paths from the output graph.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 XGPackedReferencePathOverlay
should no longer crash for short pathsvg 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.The gbwt
, gbwtgraph
, gcsa2
, libbdsg
, libhandlegraph
, libvgio
, and xg
submodules have been updated.
Published by adamnovak about 2 years ago
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:
uniform_int_distribution
unit tests no longer hang on MacOS 12vg giraffe
can now --align-from-chains
to do long-read alignmentsmake 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 onceThe vcflib
submodule has been updated.
Published by jeizenga over 2 years ago
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:
Published by jeizenga over 2 years ago
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.
Published by StephenHwang over 2 years ago
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 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.*
as the sample name as generic named paths.#<number>
after them as (pieces of) haplotypesRS
tags in GFA headers as space-separated lists of samples whose paths are references, not haplotypes.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.gbwtgraph
libvgio
libbdsg
dozeu
gfakluge
(removed)Make sure to git submodule sync
and git submodule update --init --recursive
if building from source.
Published by StephenHwang over 2 years ago
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:
vg mpmap
now distinguishes unmapped reads from reads with MAPQ 0vg mpmap
is faster on very complex cyclic graphsvg chunk -m
no longer bothers parsing Alignment
svg sim
will stop if there are too many Ns in the source graph instead of spinning foreverlibzstd
libbdsg
xg
Make sure to git submodule sync
and git submodule update --init --recursive
if building from source.
Published by StephenHwang over 2 years ago
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:
vg giraffe
can now produce GAF using GFA segment name coordinates.vg sim
no longer annotates reads with positions along synthesized haplotype pathsvg 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.gssw
libvgio
Make sure to git submodule sync
and git submodule update --init --recursive
if building from source.