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.