scorpio v0.3.19

• Updates to allow scorpio define to accept more general inputs
• Added more tests

scorpio v0.3.17

This update handles cases where parent constellations of recombinant lineages would be flagged as the 'best constellation' but not the recombinant or parent individually. This small update forces "mrca_lineage" field to not be an empty string, so whatever the best constellation other than individual parent lineages will be chosen instead.

scorpio v0.3.16

Enables alternative levels of rules within a constellation file.

This release coincides with a breaking change to constellations.
This change is required to be able to allow a probable Omicron (B.1.1.529) to exist as well as its 3 sublineages.
It remains necessary to have a probable definition while global bioinformatics pipelines continue to call for reference in low quality regions, and now there are 3 sublineages the probable definition should not only apply to BA.1.

scorpio v0.3.15

• Allows comments in constellation files
• Provides option to skip amino acid translation during scorpio define
• Classifies deletions in amino acid space slightly differently

scorpio v0.3.14

Small bug fixes:

• Fix to scorpio list where a line had been deleted
• Fix to extract_definitions.py where the info printed was not right
• Fix to type_constellations.py where the counts using --combine were not being reset between samples

scorpio v0.3.13

• Allows constellation files to be relative to a specified parent
• Add --combination option to haplotype to allow all mutations from all constellations to be typed
• Handle multiple constellation files for the same constellation name
• Allow scorpio define to give definitions relative to proteins with --protein

scorpio v0.3.12

Fix minor bugs with scorpio define

scorpio v0.3.11

Fix release versioning

scorpio v0.3.10

Add logging module
Add scorpio --list to output the constellation names found

scorpio v0.3.9

Updates to README specifying the acceptable formats for mutations
Add --dry-run option which runs classify and haplotype only up to the point where constellation files have been parsed.
Fix bug in haplotype where 2 open file handles were trying to write the same data to the same file
Exit rather than ignore if mutations specified with --mutations are not in an acceptable format