v1.3.8

DO NOT USE - PLEASE UPGRADE

This release enables the user to alter the minimum frequency for ethA mutations at protein position 237 and rpoB mutations at protein position 449. New command-line arguments are provided and the help message was organized.

v1.3.7

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This release refines the regions for tNGS and also adds a column which indicates the breadth of coverage for specific gene regions that activate CDC expert rules to the coverage report.

v1.3.6

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This release updates the lineage designation in the Looker report to use what is generated in the LIMS report instead. It also adds a new column to the LIMS report that contains the main lineage as determined by TBProfiler. It also resolves a bug when a gene had insufficient coverage but the output on the LIMS report reported predicted susceptibility.

v1.3.5

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This release enables user-modification of the minimum frequency for rrs and rrl mutations and also correct a bug when poor quality mutations were included in determining the maximum resistance interpretation when they shouldn't have been.

v1.3.4

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This patch fixes an issue where max(...) caused failures when there was nothing to maximize.

v1.3.3

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This release adjusts the tNGS regions for katG and rrs so that only rpoB is split. This also changes the logic so that any WT samples no longer have "NA" for the mutation but instead have "WT".

Readme updates were also included.

v1.3.2

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This release fixes an issue so that genes are now considered sequenced if they actually were. In addition, rule 4.2.1.3.1 now uses mdl_interpretation instead of looker_interpretation.

v1.3.1

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This release introduces the --tngs tag which changes the output columns for the LIMS report and uses a tNGS specific primer region file for the coverage report.

v1.3.0

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This minor release enables the parsing of tNGS data from TBProfiler by adding a custom bed file that only contains the genes that are sequenced in the tNGS assay.

v1.2.3

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Stable

This release can be used for WGS TB sequencing analysis. Some bugs have been identified, and it is recommended to use the latest version.

This patch release updates the LIMS lineage output.