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@xchang1 xchang1 released this 14 Feb 04:30
· 2175 commits to master since this release
v1.46.0
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Download for Linux

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:

  • Long read Giraffe codepath now falls back to non-GBWT alignment for very long tails, which is slow but at least tends to finish
  • Long read Giraffe codepath refuses to use Dozeu for tails, because the tails are very long and Dozeu will clobber the stack when given a long alignment
  • More knobs have been added to long read Giraffe to tweak what inter-pre-cluster connections are sent to reseeding, and what chains are actually made into alignments
  • vg stats now reports on time-usage information in GAM files if available
  • Wiki tutorial on programming with libbdsg and gbwtgraph is now under CI test.
  • Rescue alignment in vg giraffe paired-end mode should no longer decide it rescued off of the wrong alignments
  • GAMP files no longer lose the "secondary" annotation when converted to GAM
  • New benchmarking and read-simulating scripts for testing long-read Giraffe
  • Fixed a crash in Giraffe correctness tracking in the long-read codepath due to out-of-bounds accesses into previous stages in the funnel
  • Reading SAM/BAM/CRAM files into a graph (i,e, vg 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 threads
  • vg 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 CI now tests against sequenceTubeMap using its recommended Node version
  • vg rna will no longer in certain cases skip the first line when the annotation input has a header
  • vg rna no longer crashes when adding splice-junction from a BED file with introns
  • scripts/make_pbsim_reads.sh now works with local graph files in addition to S3 URLs
  • scripts/lr_benchmark.sh now downloads and uses CHM13 graphs
  • Chaining lookback now stops at 15 total items max
  • Tail alignment with GSSW now refuses to fill more than 16 mibi-cells
  • Fix off-by-1 array size bug in vg clipedge clipping
  • Faster vg chunk on GBZ input
  • Highly experimental vg haplotypes subcommand for sampling haplotypes based on kmer counts.
  • vg giraffe now preloads the distance index into memory before mapping any reads
  • Makefile should deal better with protoc not being installed
  • Surjecting now works for interleaved GAFs, even if one or both reads are unmapped.

Updated Submodules

The libbdsg and gbwtgraph submodules have been updated.

New Submodules

The kff-cpp-api submodule has been added.

Assets 4
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