dais-ribosome v2.1.0

Release Notes for v2.1.0 - 2026-08-04

Added

• Added a new experimental section to the TOML file, including the ability to
  rewrite genome deletions

Fixed

• Whitespace is now removed in the keys in the reference file, and empty
  reference IDs and ctypes are explicitly rejected

dais-ribosome v2.0.3

Release Notes for v2.0.3 - 2026-07-30

Fixed

• Fixed bug where timestamp was printing in UTC+0 time zone rather than in the
  system's current time zone

dais-ribosome v2.0.2

Release Notes for v2.0.2 - 2026-07-17

Added

• Library change: zoe_genome_aln is now a field of GenomeAndProductStates to provide access to the genome alignment and CIGAR string

Changed

• Unrecognized fields in the TOML file are now rejected during parsing
• Duplicate sections and keys in the codon-position weights file are now rejected
• No data may appear before the first header in the codon-position weights file

Fixes

• Fixed incorrect TOML field for try_stop_extension in the flu module, causing stop extension to not apply
• Tabs in FASTA-file query IDs are now replaced with a space in the output files
• Sections in the specs file or codon-position weights file that do not match each other or the reference file now throw an error
• Fixed stack overflow when the CDS specs have a large number of comments or blank lines
• Tabs in reference IDs are now rejected with an error
• An error is now thrown if any file is both an input and an output, or if any output files coincide
• Fixed incorrect documentation on the repairable_end_limit rule within the library
• Fixed overflow when deletions near -2 ribosomal frameshifts occur

dais-ribosome v2.0.1

Release Notes for v2.0.1 - 2026-07-10

Added

• Adds 6 argument invocation for genome-level output files

Changed

• Reverts 4 argument handling to v1 style
• We removed --skip-genome and revert to the v1 style by omitting genome args
• The codon-position weights file is now optional in the TOML, and a warning is issued by the binary if the file is unspecified or empty

Fixes

• Fixes bug causing alternative or uppercase module names to fail to load the corresponding SSWSort module
• The error message for failing to find an SSWSort module now distinguishes between the module not being present and the SSWSort resources not being present
• sswsort_res is now searched for in the same directory as ribosome_res, instead of using the current working directory

dais-ribosome v2.0.0

Release Notes for v2.0.0 - 2026-07-08

Changed

• DAIS-ribosome has been rewritten into self-contained Rust CLI app. See MIGRATION.md for changes between v1 and v2.