Releases · apcamargo/genomad

Mention the Zenodo upload of geNomad's database in README.md.
Add the following sentence for the help dialogue of the --min-plasmid-marker-enrichment, --min-virus-marker-enrichment, --min-plasmid-hallmarks, and --min-virus-hallmarks parameters: "This option will be ignored if the annotation module was not executed".
Apply a uniform prior to the empirical sample composition in score_batch_correction. This will shrink the effect of calibration when the empirical composition distribution is very skewed.
Reduce the --min-score in the README.md example to 0.7.

Fix a bug in the score calibration module where the sample size was set to a constant value and the "Your sample has less than 1,000 sequences…" warning would always appear.

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 only the major version was compared.

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