Taxpasta

Added

- Inserted columns with taxonomic information like the name, rank, or lineage of a
taxon at the beginning of the table rather than the end (86).

Fixed

- Enabled handling of MetaPhlAn profiles with taxonomy identifier -1 and combined all
unclassified entries into one with ID 0 (85).
- Generally increased the tolerance in the compositionality checks. Up to 1%
deviation are now allowed; 2% for Bracken profiles (84).

Fixed

- Fixed the version string according to hatch-vcs output (74).
- Increased the tolerance when comparing floats in the Bracken profile validation
(76).

Fixed

- Fixed how the `taxopy.TaxDb` is loaded. It was previously deleting local files and
downloading a new copy from NCBI instead (67).

Fixed

- Handled metaphlan profiles with unclassified taxa in the lineage (61).

Added

- Created command line options to expand the standard profile with name, rank,
and/or lineage taxonomic information (60).

Fixed

- Made the Krakenuniq reader more accepting (57).
- Documented _which_ columns are used in final standardised output profiles.

Fixed

- Documentation on where the taxpasta-supported Kaiju output comes from (i.e.,
`kaiju2table` rather than Kaiju itself) (54).
- Corrected the assumption that the first two entries in a kraken2 profile are
always unclassified and root node percentage of abundances. This is not the
case for profiles where 100% of reads are assigned to taxa. Kraken2 profile
validation now looks for the `'U'` and `'R'` taxonomy levels explicitly and
checks their sum.