v1.4.4.6

DO NOT USE - PLEASE UPGRADE

This release adds some additional checks to long deletions so that poor depth and read support do not falsely flag these mutations as insufficient coverage. This only needs to be done to the v1.4.4+ branch because the latest version of TBProfiler has a fix that makes these mutations no longer have 0 depth.

v1.4.4.5 was deleted because of an errant or becoming an and. The v1.4.4.5 docker image is still available.

v1.5.7

DO NOT USE - PLEASE UPGRADE

This release includes the cycloserine changes merged into the general WHO v2 branch so that I don't have to keep branching all over the place.

v1.5.6

DO NOT USE - PLEASE UPGRADE

This implements the change made in v1.4.4.4 but on this branch.

v1.4.4.4

DO NOT USE - PLEASE UPGRADE

This release makes sure that mutations from low coverage genes that have valid deletions are not ignored due to insufficient coverage, because that low coverage may be resulting form the valid deletion.

v1.5.5

DO NOT USE - PLEASE UPGRADE

This version of tbp-parser requires input from TBProfiler v6.2.0+. It also uses the updated interpretation scheme where nonsynonymous mutations are considered "U" instead of "S" (like v1.4.4.3).

Use at your own risk.

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This release fixes an issue where the highest MDL interpretation was being affected by genes that were not part of the GENES_FOR_LIMS list due to additional gene-drug combinations being added in TBProfiler v6.2.0+

v1.4.4.3

DO NOT USE - PLEASE UPGRADE

This release can be used for both WGS and tNGS TB sequencing analysis. This version requires input from TBProfiler v4.4.2. This version differs from v1.4.2.1 in that nonsynonymous mutations are considered "U" instead of "S".

Use at your own risk.

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This release fixes an issue where Pending Retest was appearing even if resistant mutations were detected.

v1.4.2.1

DO NOT USE - PLEASE UPGRADE

stable

This release can be used for both tNGS and WGS TB sequencing analysis. It requires using TBProfiler v4.4.2. It also uses an older interpretation scheme where nonsynonymous mutations were considered "S" instead of "U" (which is the case in the v1.4.4.3 release).

Use at your own risk.

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This fixes the pending retest issue in v1.4.2

v1.5.4

DO NOT USE - PLEASE UPGRADE

This pre-release fixes a bug where R LIMS calls were being overwritten.

v1.5.3

DO NOT USE - PLEASE UPGRADE

This release ensures that "mmpR5" is renamed to "Rv0678"

v1.5.2

DO NOT USE - PLEASE UPGRADE

This release fixes an edge case when the same mutation appeared twice but with different coverages, leading to both being removed due to indexing only grabbing the first item. Also, the alternate_consequences section was renamed in TBProfiler outputs to consequences.