scorpio v0.3.8

scorpio haplotype and scorpio classify now accept a list of mutations or mutations files with --mutations
These can be .txt or .csv with mutations in first column with header "id" or no header
These additional mutations are typed and if --append-genotypes is used, a column per variant is output in the relative files

v0.3.7

Fix versioning bug #21

scorpio v0.3.6

Adds --append-genotypes flag to scorpio haplotype to output column-per-variant in a file per constellation (the same file as outputs counts/scores)
Prevents scorpio define from using protein definitions in unexpected ways

v0.3.5

Adds --list-incompatible flag to scorpio classify which adds an extra column to output CSV listing anything from called constellation JSON file under key "incompatible_lineage_calls"

v0.3.4

Fix for biopython 1.74

v0.3.3

Explicity convert between Seq and string to use replace and translate functionality

v0.3.2

• Pulls in mrca_lineage field from JSON files, checks it's not got weird characters and outputs it during classify
• Handles deletions specified in AA space in AA space
• Adds pangolin mode which disregards anything in constellations/data for robustness
• Allows label to be specified on command line and uses that field for call where possible (not included in comparison if not provided)

v0.3.1

Handle labels with weird symbols in

v0.3

Add a version number to tip that works with pangolin and latest constellations definitions

v0.2

Initial release includes classify and haplotype commands from an alignment to reference