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)

TBProfiler v4.2.0

Changes

New features

• Experimental spoligotyping available (add --spoligotyping to profile command)
• Added some QC metrics to collate output (#205)
• Improved command line interface. All input file types can now be given on the to the main profile function (-1/-2: fastq, -a: bam/cram, -f: fasta, -v: vcf)

Fixes

• Fix for fasta profile (#208)

Other

• Removed pathogen-profiler code and put back into own repository (makes it easier to reuse that code for other profiling tools) https://github.com/jodyphelan/pathogen-profiler

TBProfiler v4.1.1

Change

• Fix for issue with itol output (#200)

TBProfiler v4.1.0

Updates

Thanks to everyone who submitted bug reports and suggested changes. Keep them coming :)

• Added pilon as a variant caller (#194)
• Added lofreq as a variant caller (#202)
• Updated the drug resistance types (#200)
• Update packaged db to latest version with mutations from WHO catalogue (see here)
• Fixed bug in snpEff call (#193)

TBProfiler v4.0.3

Changes

• Fixes for several bugs introduced in v4 (#187, #188 (thanks @pmenzel), #189, #190)
• Large deletions are now annotated using hgvs terminology, using gene coords (#191, jodyphelan/tbdb#21)

TBProfiler v4.0.2

Changes

• Remove temp file produced during pipeline run

TBProfiler v4.0.1

Changes

• Bug fix for critical bug introduced in v4.0.0 when installing with conda
• Update default caller to freebayes