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 that global dictionary, it will be added for the mutation and 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.

v2.1.0

tbp-parser v2.1.0

This minor release of tbp-parser deprecates all versions of tbp-parser that rely on TBProfiler versions prior to v6.0.0.

In addition, the proximal promoter regions of 60 genes are now being included in the expert rule interpretation designations.

v2.0.0

This major release migrates all of the v1.5+ changes into a major version instead of a minor. In addition, it implements the changes included in v1.4.4.10 & v1.4.4.11.

Only for use with WHO v2 and TBProfiler outputs v6.2.1+

v1.6.0

This minor release fixes an issue present since v1.4.1 where non-LIMS genes were being considered for maximum MDL drug interpretation. This corrects this issue so that only LIMS genes are considered for maximum drug interpretation.

Only for use with WHO v1 catalogue and TBProfiler v4.4.2

v1.4.4.11

DO NOT USE - PLEASE UPGRADE (v1.6+)

This release fixes a bug when no MDL interpretations are identified for a gene which led to failures with the max() function; this bug only appears after v1.4.4.10's fix that pre-screens MDL interpretations to not consider any with poor mutational quality.

v1.4.4.10

DO NOT USE - PLEASE UPGRADE

This release corrects a bug when the maximum MDL interpretation had a poor mutational quality warning that led to erroneous drug interpretaitons.

v1.4.4.9

DO NOT USE - PLEASE UPGRADE

This release adds the optional input --add_cs_lims which will add cycloserine fields to the LIMS report.

v1.5.10

DO NOT USE - PLEASE UPGRADE (v2.x+)

This release corrects the capitalization of ald and alr genes in the LIMS report.

Only compatible with TBProfiler v6.2.0+

v1.5.9

This release makes the following adjustment to lineage determination for the LIMS report for tNGS only

• The number of loci on the coverage report (there are 17, 2 for rpoB and 2 for mmpR5/Rv0678) that have at least 90% breadth of coverage in the "Coverage_Breadth_reportableQC_region" column will be counted (no change from v1.4.4.7)
• That number will be divided by the number of loci in the coverage report (of which there are 17) to get a percentage (no change from v1.4.4.7)
• MTBC ID will be determined if that percentage is greater than or equal to 70%. This means that 5 loci can be below 90% before MTBC ID cannot be detected.

Only compatible with TBProfiler v6.2.0+