apcamargo/genomad: geNomad v1.1.0

Added

• Dockerfile for version 1.0.0.
• Sequence class: add support for str in __eq__.
• Sequence class: add a __hash__ method.
• Compute marker enrichment in the marker-classification module.
• Add columns for plasmid and virus marker enrichment to the _plasmid_summary.tsv and _virus_summary.tsv files.
• Set --min-plasmid-marker-enrichment and --min-virus-marker-enrichment to 0 as default. This will alter the results when using default parameters.
• Add support for plasmid and virus hallmarks. Requires geNomad database v1.1.
• Add CONJscan annotations to _plasmid_summary.tsv. Requires geNomad database v1.1.

• Sequence class: simplify has_dtr return statement.
• Sequence class: make __repr__ more friendly for long sequences.
• Sequence class: rename the id property to accession.
• Amino acids are now written to _provirus_aragorn.tsv.
• Update the XGBoost model file to the .ubj format.
• Require xgboost >=1.6.
• The taxonomic lineage in _taxonomy.tsv and _virus_summary.tsv will use Viruses as the highest rank, instead of root.
• Change order of the columns in _plasmid_summary.tsv and _virus_summary.tsv.
• Explicitly set fraction to 0.5 in taxopy.find_majority_vote.

• tRNA coordinates are now 1-indexed.
• Write summary_execution_info.
• Fix a problem in DatabaseDownloader.get_version where it only only compared the major version.