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- Download databases from Zenodo rather than from NCBI (in order to fix versions).
- Improve I/O error messages printed by
- Improve ProPhyle code.
make helpto print a list of commands for developers
make coverageto compute code coverage
make pylintto run Pylint
- Add a Code of Conduct
prophyle compile -Ffor forcing a recompilation
- Specify recommended versions of dependencies for PyPI
make submodulesto download submodules using
- If submodules are missing from the repository, download them using
A major update. Rewritten assignment algorithm, improved tests, new classification parameters, and many fixed bugs.
- Autodetect restarted search vs. rolling window from the index.
- Add revision & commit info to
prophyle -v(using git hooks).
- Add LCA options
-X, and an option to fully mimic Kraken (
-m h1 -f kraken -L -X).
- Add an internal system of passing additional parameters (using JSON).
- Add hf and cf tags to the SAM output.
- Add h2 and c2 as measures for assignments.
- Restructure and improve tests.
- Test ProPhyle both from the package and from the repository directory.
- Improve the master Makefile.
- Make ProPhyle less verbose (especially the compilation commands).
- Improve the Kraken-like format.
- Refactor & optimize the assignment algorithm.
- Fix a FASTQ buffering bug in
prophyle_index(loading entire read sets when used with Oxford Nanopore data).
- Fix LCA-related bugs in the Kraken-like mode.
- Fix many other minor bugs in entire package.