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Cactus 2.8.1 2024-04-04
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@glennhickey glennhickey released this 04 Apr 20:47
· 261 commits to master since this release
v2.8.1
28a6e2c
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GPG key ID: B5690EEEBB952194
Learn about vigilant mode.

Cactus 2.8.1 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 patches some recent bugs, including a major bug introduced in cactus-hal2maf in v2.7.2 that could produce negative-stranded (and out of order) reference rows.

  • Do not apply RED masker to contigs that are likely to crash it (tiny contigs and extremely low information contigs)
  • Add --coverage option to cactus-hal2maf to include table of coverage statistics in the output
  • Fix bug where :start-end contig suffixes caused the pangenome pipeline to crash. They are now correctly handled as subranges
  • Turn off abPOA seeding by default, after finding (what must be a fairly rare) case where it doesn't work.
  • Improve cactus-hal2chains interface
  • Add range support to cactus-hal2maf via --start/--length or --bedRanges
  • Deprecate cactus-maf2bigmaf --chromSizes (use --halFile instead, as it handles "."s in genome names properly)
  • Fix bug where reference row could be lost in cactus-hal2maf MAF due to sorting error.
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