ChangeLog.md

2.22.4 [2024-07-31]

Fix bugs in grep, consensus, head, and tail

• grep failed when no explicit pattern was given (only patterns from -f)
• consensus failed on --table option due to incomplete implementation
• head and tail both failed when reading STDIN when using default ("-1") cutting pattern

More residual bugs from the modularization effort of the early 20s.

2.22.3 [2023-03-03]

• Fix bug in subseq

2.22.2 [2022-07-18]

• Fix bug in consensus
• Fix bug in subseq --color

2.22.1 [2021-07-19]

• fix instant death bug in cut
• add tests for cut

2.22.0 [2021-05-14]

• add --delimiter argument to clean for removing descriptions

2.21.1 [2021-02-15]

• fix bug in translation of gapped DNA sequences

2.21.0 [2020-09-14]

• modularize functions for import into other Python packages
• make the subseq annotation optional ("|subseq(i..j)")

2.20.0 [2020-09-03]

• draft modularization

2.19.0 [2020-07-29]

• change smof uniq --final-header to --first-header and keep first header rather than last
• add smof uniq --removed=FILE option that writes removed entries to FILE

2.18.0 [2020-03-02]

• allow lowercase 'X' to be replace with 'n' in clean standard function
• raise warning when character type is not specified in clean standard function
• add --cds option to translate that returns DNA coding sequences

2.17.0 [2019-12-31]

• force order to be retained in uniq -f

• add 'standardize' option to clean that replaces 'X' in DNA with 'N' and standardizes gaps from [._-] to just '-'