v1.0

Release to accompany the Afanc paper.

Key changes:

• Bayesian lineage classified instead of the canonical SNP implementation.
• Adds Bayesian lineage classification to the screen workflow when matching profile models are available.
• Adds a standalone afanc classify module for classifying existing VCFs or Ardal-style allele JSON payloads.
• Adds an autodatabase assembly manifest workbook describing provided assemblies, taxa, tax IDs, inclusion/rejection status, QC outcomes, and Mash metrics.
• Tidied up the output report.

v0.11-alpha

• Moved from using the old Entrez esearch utility to the new ncbi datasets tool.
• no_map mode now produces a final report.
• fixed some of the function names.

v0.10.2-alpha

jsons files in the database now use relative paths.

v0.10.1-alpha

• fixed a bug which comes about as a result of the naming convention used in the input fasta database differing from that used in the ncbi taxonomy database

v0.10.0-alpha

• Variant profiling module implemented.
• Clustering and Variant profiling results reported.
• More accurate and robust clustering approach using elastic thresholding and a Bayesian approach to variant level taxon hit detection

v0.9.2-alpha

• Fixed a bug where the final JSON creation fails if the top hit is higher than species level, and therefore has no genome associated with it to map to.
• Version numbers for all python packages, software dependencies, and NCBI taxonomy DB are now captured in either a separate JSON (autodatabase) or in the final report JSON (screen).

v0.9.0-alpha

• New Local threshold algorithm for higher fidelity variant level calling.
• Scoring for variant level taxa which were called using the local threshold.
• Test dataset included.

0.8.0-alpha

Version for Lodestone UAT.

v0.7.1-alpha

Release for Lodestone fork

v0.7-alpha

Includes the get_dataset module.