Sam2lca

- escape the case that there are no reads that pass the minimal percent identity threshold

- Performance improvement when writing bam split by TAXID

Patch release for 1.1.0: Fix the index of bam alignment sam2lca output files when split by rank

- Added the option to split bam ouput file by TAXID at specified rank

Added

- Added sam2lca tutorial
- Add Custom acc2tax with json
- Total number of reads is computed early on to provide progress bar
- unit and integration testing with PyTest
- Total Descendant read counts for each taxon
- GTDB taxonomy and acc2tax added
- 18s acc2tax added
- XN and XR flag in bam output for, respectively, Taxon name and rank
- Add edit distance threshold filtering

Changed

- Code refactoring for speedup, making use of multithreading on shared dictionaries
- Improve logging and replace prints statements with logging.info
- ete3 has been replaced by taxopy
- Unclassified TAXID is now `12908` by default
- RocksDB params changed
- TAXID of LCA is only attributed to alignment segments passing threshold
- Identity threshold is now a range selection in CLI.

Dependencies

- ete3 removed
- ordered-set removed
- pytest-console-scripts 1.3.1
- scipy
- Jinja2 pinned version ot 3.1 (see [RTD issue](https://github.com/readthedocs/readthedocs.org/issues/9038) )

Removed