Mirmachine

Changed
- cmsearch --incE 0.2 argument is added to the cmsearch command.
- fewer than 50 nucleotides are not considered as a hit anymore.
- GFF files have "MirMachine" and "microRNA" fields that replaced the previous fields.
- Some bug fixes and improvements.
Added
- microRNA score reported in GFF files.
- microRNA losses reported in GFF files
- Seed match reported in FASTA headers with seeds.

Changed
- Minor change, heatmap file node, query_node update

Changed
- MirGeneDB v2.1(2022)
- Proto: 143 but 326 models available
- Deutero: 388 but 825 models available
- Combined: 509 but 1157 models available
Added
- Some minor additions.

Added
- Family and node printing.
- Exception handling for wrong model selection.
- Exception handling for single family mode.
Changed
- New header for GFFs.
- Snakemake workflow update to better handle output files.

Changed
- Bioconda installation problem is fixed by updating requirements.txt.

Added
- Some features were added to main executable such as printing ascii tree, nodes etc.
Changed
- Tree parser now using re.search function. This can potentially cause a different behaviour.