1.4.2

Small update to make sure freyja --version gives the correct version.

1.4.1

Adds read analysis tools for mutation cluster detection and visualization, as well as mutation specific read extraction/filtering.

Also adds barcode version checking via freyja demix --version.

1.3.12

Uses updates downloaded from repo by default (updated and recorded with github action). Adds weekly plot interval, reverses legend order to match plot. Also adds flexibility to add lineages that aren't observed in public data (i.e. gisaid-only).

1.3.11

Add relative growth rates, improvements to dash.

1.3.10

moves lineage metadata downloading to freyja update, defaults to cov-lineages lineage list (to handle issue of asynchronous lineage lists at UShER and cov-lineages, pulls lineage data from patched lineage.yml from outbreak.info

1.3.9

Enables custom lineage grouping, colors, ordering in dash. Fixes bugs in dash.

1.3.8

Adds robustness to freyja dash command

1.3.7

adds dashboard output functionality

1.3.6

Adds sequencing coverage estimates and --confirmedonly option to freyja demix.

1.3.5

removes warnings for more recent versions of python, adds some barcoding functions to future proof (for cases of many distinct mutations at a site over time)