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

TBProfiler v6.1.0

Changes

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

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

TBProfiler v6.0.0

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

TBProfiler v5.0.1

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

TBProfiler v5.0.0

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

TBProfiler v4.4.2

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)

TBProfiler v4.4.1

Changes

• Added dsk in kmer counting options
• Added --temp into arguments to specify temp directory (#248)
• Added spoligotype into collate (#234)
• Fixed cross-link error (#248)

TBProfiler v4.4.0

Changes

• PacBio now available as an option for --platform (#238)
• Added in --snp_dist as an option to find closely related samples using snp distance cutoffs
• The load_db function has been put back in
• The key gene_associated_drugs now in output json for drug resistant variants