Changes

• Fix for #402
• New plugin class

Changes

• Create new class-based docx templating allowing plugins to be installed
• Default behaviour for rules is to just add a comment

What's Changed

New Features

• Fixed overcalling of frameshifts in fbiC
• Packaged database updated
• Added schema versioning to result json
• Added docx output plugins

Bug fixes

• Fixed missing positions section in txt output
• Fixed issue where collate gave an error when running with only La lineage sampless

Documentation

• itol collate readme by @marvinkobit in #364

Full Changelog: v6.2.1...v6.3.0

What's Changed

• Fixed bug with samclip not being used #357
• Fixed lineage prediction error
• Fixed bug in update_tbdb #337

Full Changelog: v6.2.0...v6.2.1

Changes

• Replaced fabG1 promoter mutations with inhA as the gene name in the default database
• Small bugs fixed

Changes

• Inclusion of lineage SNP information
• Fix for empty fields in text output (#334)

Full Changelog: v6.0.0...v6.1.0

What's Changed

• Use of pydantic data models
• New database with whov2 mutations added
• Epistasis rules
• Improvements on databse flexibility
• 313 fix create db and load library by @ryanjameskennedy in #318

Full Changelog: v5.0.1...v6.0.0

Changes

• Implement sqlite3 db locking with https://py-filelock.readthedocs.io/en/latest/index.html. This should fix issues using it over nfs.
• Fix bug with phylogenetic functions from fastq data #304

Changes

• Phylogenetic functionality with usher and iqtree
• Added hard and soft filtering for variants
• Use sqlite3 db to store snp difference from reference
• Remove PDF support
• Possibility to use user-defined python function to update results (e.g. can be used to fix mmpL5/mmpR5 homoplasy)
• Added tb-profiler-tools script which will be used to add functions that are not core to tb-profiler

Changes

• Ability create a docx result output using --docx /path/to/template. A template containing jinja-like variable tags has to be supplied
• Flag --kmer_counter can be used to select alternate kmer counters for spoligotyping
• Allow for any number of spcers to generate octal code
• Fix for Invalid cross-device link errors (#268)