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Release vg 1.67.0 - Vetria · vgteam/vg · GitHub
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Don't forget to mark the static binary executable:
chmod +x vg
Docker Image: quay.io/vgteam/vg:v1.67.0
Buildable Source Tarball: vg-v1.67.0.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:
- GAF path end positions are calculated correctly in some edge cases.
--keep-path
can now be used multiple times in vg modvg giraffe --track-correctness
should no longer crash when read truth positions are on paths that exist in the graph, but are too short to reach where the read is.- Bring
vg cluster
up-to-date: now accepts GBZ files, can do short-read or long-read giraffe, and allows--prefix
for better compatibility withvg autoindex
- Add some options to
vg cluster
to help with chaining issue diagnosis: print out cyclic snarl sizes, seeds with high hit amounts - Fix GFA haplotype sniffing for GFAs with P-lines
- Use graph metadata and not path name to determine reference/haplotype status for paths in
vg call
andvg deconstruct
. - Loading transcript files will now produce a human-readable error message when there are duplicate transcripts with the same ID on different paths.
- The GBWT built while sorting GAF with
vg gamsort
is now forward-only by default. vg sim
now can output in FASTQ format via--fastq-out
- Make
vg mod -t
take an argument and stop-E
from requiring one - In
vg chunk
, fix the long names for-P
,-c
,-r
, and-R
, and make the latter two accept arguments. - Register command line options correctly & put them under test (
scripts/check_options.py
). This involved a lot of minor bugfixes and helptext modifications, collected in a Google Doc. - Manually wrap option helptext lines after 80 characters
vg sim
now works with sample name even when no GBWT is provided.- CI now enforces the minimum required GCC version.
- vg now requires a minimum GCC version of 7, the oldest major version available in the Ubuntu releases we test on for CI.
vg giraffe
usage example now shows using a.zipcodes
file and a.withzip.min
file.- vg can now be built with the mimalloc allocator (v3 beta)
Updated Submodules
- BBHash
- libbdsg
- libvgio
- sdsl-lite
- sparsepp
- vcflib
New Submodules
- mimalloc
Removed Submodules
- fastahack (now used via vcflib)
Assets 5
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