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

TBProfiler v4.3.0

Changes

New features

• Switch to jinja2 templating engine to produce text output. Also allows user to supply custom template with --output_template
• New function to list all loaded databases list_db
• Argument to prevent overwriting in create_db if db with same name already exists --no_overwrite
• New batch function to help batch run samples with a CSV as input
• Added spoligotype name annotations (#219)

Minor fixes

• Added spoligotype/rd information back into text report (#222)
• Fixed use of suspect api (#225)