vg 1.75.0 - Spike

Known Issues

In this release, the single-command haplotype sampling mode of vg giraffe will include kmc k-mer counting logs in the alignment output files, corrupting them. This issue is fixed in #4938.

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.75.0

Buildable Source Tarball: vg-v1.75.0.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:

• Put back the code to finalize giraffe's paired end distribution after trying enough reads.
• vg CI builds of ARM containers should no longer segfault when upgrading libc
• Alignment scoring and mapping quality computation have been broken out of GSSWAligner and moved to AlignmentScorer and MappingQualityCalculator.
• vg depth will now work on .gbz files.
• vg stats returns correct aggregate stats even when some values are negative
• vg filter --tsv-out has a softclip_total option for convenience (softclip_end + softclip_start)
• Speed up minimizer index construction.
• The vg giraffe --rec-penalty-chain parameter has been split into --rec-penalty (for chaining), --rec-consistency-bonus (a bonus for haplotype consistency used during chaining but not incorporated into the chain score), and --rec-penalty-aln (used to penalize alignment scores per recombination).
• Recombination-aware minimizer indexing is now always on when there are few enough haplotypes and the GBZ being indexed is not a path cover. Passing --rec-mode to vg minimizer now just makes it fail if recombination-aware minimizer indexing isn't on (because of too many haplotypes or the presence of synthetic path cover paths).
• Recombination-aware mapping is now the default in vg giraffe, if a recombination-aware minimizer index file is loaded and you are using the hifi or r10 presets. To turn it off, pass --no-rec-mode. There's no longer a distinction between .path minimizer and zipcodes files and normal ones.
• The hifi and r10 presets for vg giraffe have been updated with tuned recombination penalty settings.
• vg giraffe no longer produces alignments with nonempty path and negative or zero score. Potential alignment that would reach or go below a score of 0 (perhaps because of --rec-penalty-aln) will be removed, and if needed an unmapped alignment record will be emitted for the read.
• Significant time and memory optimizations to vg giraffe chaining/long-read mode
• --comments-as-tags is now under test with vg giraffe's chaining codepath
• Surject tests now test SAM tags in GAM with an actual vg surject command line
• vg surject now preserves unrecognized GAF tags as tags on output alignments (and GAF input in general retains tags)
• vg giraffe chaining mode now properly retains input tags on unmapped reads
• vg giraffe --track-provenance should no longer crash with complaints about the filters. (Fixes an unreleased regression.)
• Add option vg filter --tsv-out "is_aligned" to return whether a read has an alignment
• Add new vg giraffe filter for low-scoring MAPQ 0 R10 reads
• vg stats -a reports aggregate bp/alignment stats as per aligned reads, ignoring unmapped reads
• Remove --item-scale and --points-per-possible-match from vg giraffe as needless unused complexity.
• vg giraffe chaining mode allows negative affine-gap alignment scores to be log-gap rescored before tossing out negatively scoring alignments (minor accuracy improvement)
• vg now uses an old version of the multi-arch support container in its CI Docker builds to work around tonistiigi/binfmt#298
• vg find -Q/--paths-named is now deprecated due to its partial-Protobuf output
• vg find will now index its target paths but not other haplotype paths.
• vg should no longer position-index haplotype paths unnecessarily in commands using the PathPositionOverlayHelper.
• vg filter can accept GAMPs when it's told to expect them, and errors nicely with --input-mp-alns --tsv-out

Updated Submodules

Thegbwtgraph, libbdsg, and libvgio submodules have been updated.