Releases: prophyle/prophyle
Releases · prophyle/prophyle
ProPhyle 0.3.3.2
ProPhyle 0.3.3.1
Update dependencies
ProPhyle 0.3.3.0
New features:
prophyle footprint
for estimating the required memory footprint
Enhancements:
- Integer ranks
- fastapath renamed to path
- Improved tests
- Refactoring
- Updated docs
- ln tag added to outputs
Closed issues
ProPhyle 0.3.2.0
Fix many bugs and implement new features including
- Argument list too long (propagation) #301
- prophyle decompress – "tar: could not chdir to 'database/sparc1_k18'" #312
- No LCA computation in case of tie #315
- prophyle_assignment: not enough values to unpack (expected 2, got 1) #320
- RecursionError: maximum recursion depth exceeded while pickling an object #337
- Error: /bin/bash: /bin/cat: Argument list too long #350
- Add a param to stop after k-mer propagation #353
ProPhyle 0.3.1.0
Improvements
- Download databases from Zenodo rather than from NCBI (in order to fix versions).
- Improve I/O error messages printed by
prophyle_assembler
. - Improve ProPhyle code.
ProPhyle 0.3.0.3
New
- Add
make help
to print a list of commands for developers - Add
make coverage
to compute code coverage - Add
make pylint
to run Pylint - Add a Code of Conduct
- Add
prophyle compile -F
for forcing a recompilation
Improvements
- Specify recommended versions of dependencies for PyPI
ProPhyle 0.3.0.2
Fixes
- Fix the order of SAM headers in the output of
prophyle classify
.
ProPhyle 0.3.0.1
New
- Add
make submodules
to download submodules usingcurl
.
Improvements
- If submodules are missing from the repository, download them using
curl
during compilation.
ProPhyle 0.3.0.0
A major update. Rewritten assignment algorithm, improved tests, new classification parameters, and many fixed bugs.
New
- Autodetect restarted search vs. rolling window from the index.
- Add revision & commit info to
prophyle -v
(using git hooks). - Add LCA options
-L
and-X
, and an option to fully mimic Kraken (-M
=-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.
Improvements
- 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.
Fixes
- 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.