v2.4.4

tbp-parser v2.4.4

This release fixes a bug where the default bed files used for the coverage report were not able to be accessed.

v2.4.3

DO NOT USE - PLEASE UPGRADE

tbp-parser v2.4.3

This release fixes a small typo in Row.py where "No WHO confidence" should be "No WHO annotation". This fixes an issue when there is a mutation not in the WHO catalogue.

v2.4.2

DO NOT USE - PLEASE UPGRADE

tbp-parser v2.4.2

This release ensures that expert rules are implemented for mutations that were not found in WHO catalogue, which is in response to a change in TBProfiler as described in issue #20.

v2.4.1

DO NOT USE - PLEASE UPGRADE

tbp-parser v2.4.1

This release fixes the Dockerfile and updates the documentation as well as improve logging.

v2.4.0

DO NOT USE - PLEASE UPGRADE

tbp-parser v2.4.0

This release allows for the addition of a config YAML that will allow the user to overwrite the global variables and any command-line provided input parameters.

Additionally, globals was replaced by globals_ to avoid conflicting with the Python built-in globals namespace.

v2.3.0

tbp-parser v2.3.0

This release reworks the lineage designation for the LIMS and Looker reports so that if TBProfiler detects a lineage, it is reported regardless of sample quality. If no lineage has been reported by TBProfiler, the percentage of genes in the LIMS report that are above the breadth of coverage threshold is greater than a 0.7 (for both WGS and tNGS), then the lineage will be designated as M. tb.

In addition, the various pytests that confirm proper functionality have been fixed and reactivated in the Docker image.

v2.2.2

tbp-parser v2.2.2

This release removes the high-level and low-level resistance comments from the LIMS report

v2.2.1

tbp-parser v2.2.1

This release fixes a bug where rifampicin was not being renamed to rifampin and caused duplicate rows. The debug output was also tidied.

v2.2.0

tbp-parser v2.2.0

This release removes the following drug-gene combinations from the globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME dictionary:

• gyrA and gyrB:
  • ciprofloxacin
  • fluoroquinolones
  • ofloxacin
• rrs:
  • aminoglycosides

In addition, if a drug is missing in the TBProfiler JSON's gene_associated_drugs field that can be found in our internal dictionary (globals.GENE_TO_ANTIMICROBIAL_DRUG_NAME), it will be added for the mutation. The source field will indicate it was added separately from TBDB.

v2.1.1

tbp-parser v2.1.1

This patch release fixes a bug where mmpR5 was not being properly renamed to Rv0678 and a scenario where mutations that did not have identical positions were being compared.

The comment and source field from TBDB are now also included in the Laboratorian report.