Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Changed

Backwards incompatible change: now uses primer coordinates. The amplicon (and primer) information must be given in a JSON file, instead of the previous BED file.
Added command line option --reads_per_amp_dir
When building consensus from contigs, if a contig does not map then remove the contig and carry on, instead of aborting the entire assembly
Rewrite overlapper to use more amplicons, and also use more of each amplicon (less trimming at ends). New method is more tolerant of failed amplicons, still keeping adjacent amplicons.

Removed

Removed the command line function viridian amplicon_overlap.

Fixed

Handle whitespace in sequence name line of input FASTA file
Bug fix when using the option --minimap_opts. It was used for initial read mapping, but not for each racon iteration. Now used for racon iterations as well.
Fixed case viridian would crash when no amplicon contigs map, and so no consensus sequence was made. Now it finishes, with "made_consensus": false and "consensus": null in the output JSON file.
Fixed where Racon could sometimes silently fail due to how reads were sampled for an amplicon, resulting in no sequence for that amplicon.