- Used a single integer to store gene and read information in the ordinal mapper; use bitwise operations to parse the information. This significantly reduced memory consumption (#142).
- Improved alignment file processing efficiency (#153).
- Updated installation protocol. Currently a single
pip installcommand should suffice (#145). - Updated GitHub Actions test from Python 3.6 to Python 3.8. The program itself should continue to support Python 3.6+ (#158).
- Added a naive algorithm for read-gene matching when the number of reads is small. This improves speed (#148).
- Added support for stdin as input. This lets the program take a variety of previously unsupported alignment formats (#155).
- Added or updated several pieces of documentation, such as a RefSeq tutorial (#157).
- Experimentally added a much accelerated ordinal mapper, powered by NumPy and Numba (branch
numba) (#152).
- Migrated from Travis CI to GitHub Actions (#127).
- Made
--map-as-rankdefault when only mapping file(s) are provided (#132). - Renamed
--normalize|-zas--frac|-f(#128). - Modified core algorithm which slightly improved performance (#124).
- Added
tool normalizecommand, with multiple features (#124). - Added the feature to collapse a stratified table (#126).
- Created an WoL FTP server, and added link to it (#118).
- Added an WoL standard operating procedure (
wolsop.sh) and documentation (#116). - Added first citation of Woltka (#111).
- Added protocols for Bowtie2 / SHOGUN and Fastp (#121).
- Added discussion about mapping uniqueness (#131).
- Fixed free-rank classification subject not found issue (#120).
- Corrected paths to example files and directories (#117).
- Updated Qiita documentation (#107).
- Renamed "gOTU" with "OGU" (#104).
- Published at PyPI. Can be installed by
pip install woltka(#108). - Added instructions for using MetaCyc and KEGG (#99, #101).
- Added
tool collapsecommand, which supports one-to-many classification (#99).
- Fixed Handling of zero length alignment (#105).
- First official release.