Changes

• Fix compilation for M1 by @karel-brinda in #400
• Update dependencies

Full Changelog

0.3.3.1...0.3.3.2

Update dependencies

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

• Unclassified reads are missing from the SAM output #324
• Re-running finished decompression damages .bwt #329
• Add prophyle footprint #322
• Add the ln tag #297
• propagation clean: Argument list too long #292

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

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.

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

Fixes

• Fix the order of SAM headers in the output of prophyle classify.

New

• Add make submodules to download submodules using curl.

Improvements

• If submodules are missing from the repository, download them using curl during compilation.

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.