Releases: jodyphelan/TBProfiler
Releases · jodyphelan/TBProfiler
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
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