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Cactus 2.8.2 2024-05-09
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@glennhickey glennhickey released this 09 May 13:29
· 215 commits to master since this release
v2.8.2
2126683
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Cactus 2.8.2 is available in the following forms:

WARNING: do not use the github automatically generated source files (Source code (zip) or Source code (tar.gz)), these are not correct.

The Docker images and binaries linked above are built using AVX2 extensions, and require a CPU that supports them, except the "Pre-compiled Binaries For Older CPU Architectures" which should be compatible with any 64-bit architecture (and, since version 2.3.1, support Cactus's pangenome pipeline).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

Release Notes

This release fixes some bugs and adds a (docker-only) vcfwave normalization option for pangenomes.

  • Use correct bigChain.as that allows chain scores to be huge (instead of capping them)
  • Update odgi, vg, abPOA and taffy to their latest releases
  • Fix cactus-hal2maf and cactus-pangenome --odgi to work with --binariesMode docker
  • bcftools norm -f now run by default on all non-raw VCF outputs (toggle off in the config)
  • vcfwave normalization option added for pangenomes (to mimic what was done for release HPRC graphs). Note that vcfwave is not included in the binary release -- you need to use the Cactus docker or build it yourself.
  • Minigraph fasta file renamed from .gfa.fa to .sv.gfa.fa to be less confusing
  • Gap and empty MAF block filtering moved from cactus-hal2maf to cactus-maf2bigmaf. So MAF output will now have a reference base for every position.
  • Fix cactus-preprocess to do only RED masking by default (there was previously a bug where it ran RED then lastz after). The --maskMode option is also fixed to work properly.
  • Update to Toil 6.1.0
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