TBProfiler v6.6.3

Changes

• bugfix for wrong version reported with --version

TBProfiler v6.6.2

Changes

• Fix typo leading to downstream tools breaking

TBProfiler v6.6.1

Changes

• Fix typo (#424)
• Add empty 'source' and 'original_mutation' fields to annotation dictionary (#424)

TBProfiler v6.6.0

Change

Important

This version update changes the implementation of the epistais rule which may change the resistance predictions for bedaquile, clofazimine and kanamycin. Resistance is new reported unless an abrogating variant is completely fixed (100% frequency in reads). If frequency is 10% than the frequency of the abriogating variant, a note is made indicating that the episatis rule may not apply.

• Updated system for providing epistasis rules
• Add generic profile plugin
• Update conda file
• Updated the default docx template
• Add software and versions to output

TBProfiler v6.5.0

Changes

• replace fa2vcf
• make multisample vcf processing parallel
• fix typo in default template

TBProfiler v6.4.1

Changes

• Fix for #402
• New plugin class

TBProfiler v6.4.0

Changes

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

TBProfiler v6.3.0

What's Changed

Important

This is a critical update that will change resistance calls in some samples. It fixes an issue where frameshifts were called in fbiC leading to delamanid and pretomanid resistance calls (see this issue for more)

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

TBProfiler v6.2.1

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

TBProfiler v6.2.0

Changes

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