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AMR Variant detection - Parsers to be updated #70

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cimendes opened this issue Jan 4, 2022 · 1 comment · Fixed by #76 or #77
Closed
22 tasks done

AMR Variant detection - Parsers to be updated #70

cimendes opened this issue Jan 4, 2022 · 1 comment · Fixed by #76 or #77
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enhancement New feature or request help wanted Extra attention is needed p0

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@cimendes
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cimendes commented Jan 4, 2022 •
edited by fmaguire
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The following parsers need to be updated to comply with the new spec:

The following parsers currently are skipping the variant detection results:

The following parsers should be added:
@cimendes cimendes added enhancement New feature or request p1 help wanted Extra attention is needed labels Jan 4, 2022
@cimendes cimendes added p0 and removed p1 labels May 13, 2022
@cimendes cimendes mentioned this issue May 16, 2022
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@cimendes cimendes linked a pull request May 16, 2022 that will close this issue
Update parsers with new schema version #76
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cimendes commented May 16, 2022 •
edited by fmaguire
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Missing sanity tests:

  • startAMR
  • resFams

fmaguire added a commit that referenced this issue Aug 17, 2022
@fmaguire
Add mutational parsing for AMRFinderPlus #70
fb977c2
fmaguire added a commit that referenced this issue Aug 20, 2022
@fmaguire
Add RGI parsing for variants in main mode #70
c74a1b7
fmaguire added a commit that referenced this issue Aug 20, 2022
@fmaguire
Add Ariba variant parsing for #70
bc81a3d
fmaguire added a commit that referenced this issue Aug 21, 2022
@fmaguire
Add staramr variant and sanity #70
4c502a7
@fmaguire fmaguire mentioned this issue Aug 21, 2022
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enhancement New feature or request help wanted Extra attention is needed p0
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Update parsers with new schema version pha4ge/hAMRonization
Update parsers pha4ge/hAMRonization
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@cimendes