1.5.2

• Adds non-SARS-CoV-2 pathogen updating and demixing, via the --pathogen flag.
• Bug fixes, including np.float() error observed on some configurations

1.5.1

• changes default solver to clarabel, with options to use ecos and osqp
• improvements to the covariants function
• small bug fixes, plotting improvements
• switches barcodes to feather format, for faster loading and smaller file size.

1.5.0

• adds --depthcutoff features to account for available genome coverage, de-aliasing, and assignment of MRCAs
• enables both true and relaxed MRCA assignment
• incorporates collapsed MRCAs into summarization and plotting
• some small speed improvements
• option to set variants threshold above 0 for space constraints

1.4.9

Includes a series of updates:

• Improved error message reporting to prevent hard to understand fail cases
• Dash and plot changes to prevent labels/legend from being cut off
• spike (or arbitrary genome region) coverage estimates
• options to retain intermediate outputs via dash/plot
• lineage hierarchy input for demix, plot, dash, relgrowthrate

1.4.8

Bug fixes, plus beta version of adaptive regularization method.

1.4.7

Fix issue with freyja update

1.4.6

Update barcodes

• Now pulls barcodes from GISAID tree by default

Variants

• Added option to include amino-acid annotations
  plot-covariants

Plot Covariants

• Now creates heatmap plots, showing the frequency of each covariants pattern.

---

• Additional minor fixes

1.4.5

Adds lineage collapse functionality to account for sequencing coverage (using the --depthcutoff option in freyja demix). Small fixes to covariants.

1.4.4

Fixes plot issues, metadata parsing issues (thanks @tkchafin !), refines methods for covariants and associated plotting in plot-covariants.

1.4.3

Fixes to freyja covariants. beta addition of barcode_build function. Small bug fixes for freyja plot.