v1.5.1

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This release implements the same change in v1.4.4.2 but on the who-v2 branch.

v1.4.4.2

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This release fixes an issue where "No sequence" in the gene code for the LIMS report was not triggering the antimicrobial code to switch to "Pending Retest".

v1.5.0

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This pre-release includes necessary nomenclature changes that are introduced by using the outputs from TBProfiler v6.2.0.

v1.4.4.1

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This release modifies the coverage threshold for LIMS ID designation to a default of 90 instead of whatever value is used for QC.

v1.4.4

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This release updates the interpretation outputs of several instances; primarily, any nonsynonymous mutation that is NOT an upstream gene variant is now consider "U" for both MDL & Looker interpretations. Also, loss of function mutations in katG, pncA, ethA, and gid now are considered "R" instead of "U".

v1.4.3

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This release implements tNGS specific lineage determination by checking if p.His57Asp is present in pncA.

v1.4.2

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This release fixes and issue when "Pending Retest" appears in the LIMS report but shouldn't, and addresses an issue when rpoB reads "no sequence" when outside the expected region.

v1.4.1

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This release fixes the following issues:

• when mutations are outside of the expected region and spurious rpoB coverage values appearing
• when a deletion fails in the position QC but not in locus QC
• when the highest MDL interpretation was being overwritten incorrectly
• when "No Sequence" in the LIMS gene code did not cause the antimicrobial code to say "Pending Retest"

v1.4.0

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This minor release changes the way QC is performed by altering the order of operations and changing the outputs of the LIMS report based on the specific QC fail message.

v1.3.9

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This release creates additional command line arguments that adjust the QC minimums for rrl and rrs further. A bug was also fixed when mutations in rpoB fell outside the expected regions.