AMR Variant detection - Parsers to be updated
Closed this issue · 1 comments
cimendes commented
The following parsers need to be updated to comply with the new spec:
- AmrFinderPlusIO.py
- AmrPlusPlusIO.py
- RgiIO.py
- AbricateIO.py
- AribaIO.py
- CSStarIO.py
- DeepArgIO.py
- GrootIO.py
- KmerResistanceIO.py
- MykrobeIO.py
- ResFamsIO.py
- ResFinderIO.py
- SraxIO.py
- Srst2IO.py
- StarAmrIO.py
- TBProfilerIO.py
The following parsers currently are skipping the variant detection results:
- AmrFinderPlusIO.py
- AmrPlusPlusIO.py: this tool more tells you that you should check for SNPs in certain genes so I'm inclined to not include variant parsing for it.
- RgiIO.py
- AribaIO.py
The following parsers should be added:
cimendes commented
Missing sanity tests:
- startAMR
- resFams