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CHANGELOG.md

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Changelog

[4.0.0] - 2024-04-22

Added

  • Support for background variants
  • Support for out-of-frame CDS targeton regions whose 5' and 3' extensions span both adjacent and distal bases
  • CLI: add --include-no-op-oligo option to the sge subcommand
  • CLI: add --bg option to the sge subcommand
  • CLI: add --force-bg-ns option to the sge subcommand
  • CLI: add --force-bg-indels option to the sge subcommand
  • CLI: add --bg-mask option to the sge subcommand
  • Configuration: add includeNoOpOligo attribute
  • Configuration: add backgroundVCFFilePath attribute
  • Configuration: add forceBackgroundNonSynonymous attribute
  • Configuration: add forceBackgroundFrameShifting attribute
  • Configuration: add maskBackgroundFilePath attribute

Changed

  • Minimum Python version: 3.11
  • Mutator: deletion pattern span and offset can be set to any valid value
  • Metadata table: report the type of mutation for the aa, ala, and stop mutators (mut_type field)
  • Metadata table: in cDNA mode, mutations preserving stop codons are now annotated as nonsense (vs. synonymous)

Fixed

  • Fix codon tables loaded from files where the codons are not grouped by amino acid

[3.0.1] - 2023-07-18

Added

  • Docker: add ps executable to support NextFlow

Fixed

  • Fix custom variants being ignored when no targeton region is set as mutable
  • Fix error on mutations that end but do not start in codons affected by PAM protection edits
  • Metadata table: fix MAVE-HGVS strings (mave_nt field) to correctly report as deletion-insertions those deletions that occur in codons affected by PAM protection edits where the edit itself is preserved

[3.0.0] - 2022-10-11

Added

  • CLI: add --config option to main command
  • CLI: add --min-length option to both subcommands
  • Metadata table: add mseq_no_adapt field
  • Metadata table: add pam_mut_annot field
  • Metadata table: add pam_mut_sgrna_id field
  • Metadata table: add mave_nt field
  • Metadata table: add mave_nt_ref field
  • Metadata table: add vcf_var_in_const field
  • Output files: generate additional VCF file where REF does not include PAM variants
  • Output files: generate JSON file reporting the execution parameters

Changed

  • CLI: enable main command to run from configuration
  • Output files: extend the REF of the entries in the output VCF to include the PAM variants occurring at the liminal codons, if any

Fixed

  • Fix the REF of custom substitutions and deletions to include PAM variants, if any (this may affect oligonucleotide names)

[2.0.0] - 2021-07-12

Added

  • Add cDNA DMS library design as cdna subcommand

Changed

  • Move SGE library design to sge subcommand
  • Lock dependency versions
  • Make unique oligonucleotide name selection order-invariant

Fixed

  • Fix discarded metadata column order and filtering

[1.0.0] - 2020-12-21

Initial release.