@karel-brinda karel-brinda released this Nov 17, 2017 · 76 commits to master since this release

Assets 2

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.

@karel-brinda karel-brinda released this Nov 11, 2017 · 98 commits to master since this release

Assets 2

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

@karel-brinda karel-brinda released this Nov 2, 2017 · 147 commits to master since this release

Assets 2

Fixes

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

@karel-brinda karel-brinda released this Oct 29, 2017 · 150 commits to master since this release

Assets 2

New

  • Add make submodules to download submodules using curl.

Improvements

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

@karel-brinda karel-brinda released this Oct 25, 2017 · 155 commits to master since this release

Assets 2

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.
Jul 22, 2017
Merge pull request #238 from karel-brinda/update_docs
Update docs

Former-commit-id: 489d6a4