Samestr

Minor Updates:
- fixed some bugs introduced in 2024.1
- Databases generated and uploaded to Zenodo

Major Updates:
- Support for [mOTUs](https://github.com/motu-tool/mOTUs) markers (v2, 2.5, 3, +)
- Support for MetaPhlAn SGB-level markers (mpa_vJun23_CHOCOPhlAnSGB_202307, mpa_vOct22_CHOCOPhlAnSGB_202212, mpa_vJun23_CHOCOPhlAnSGB_202307, +)
- Database has improved footprint, structure, integrity check

Minor Updates:
- Rewrite to support custom databases in the future
- Changes in command options

Performance

- Reverted the switch to pysam during bam-to-pileup conversion, as it was fine with smaller test datasets but significantly slower and RAM hungrier than the cli samtools install. Improved performance of conversion step.

Features
- Support for pypi installation
- [pending] preparation for bioconda installation

Bugfixes
- Bugfixes of Python 3.9 rewrite
- Fixed tmp dir specification

Other
- Output structure of `samestr convert` now follows the style of the other commands

Features
- This is a rewrite of SameStr in Python 3.9
- Native support for MetaPhlAn v3 and v4 objects and profile formats, addresses 5

Features
- Workaround for compatibility with MetaPhlAn v3 and v4

Bugfixes
- Fixed min. coverage calculation (now greater or equal, not greater)
- Clarified documentation of MetaPhlAn v3/v4 compatibility workaround

Other
- Updated citation