Update parsers with new schema version #76

cimendes · 2022-05-16T08:56:47Z

Closes #70

…use constants

cimendes added 11 commits May 13, 2022 17:30

update abricate (and sanity test)

bc74a1d

update amrfinder (and sanity test)

5b73fcc

update amrplusplus (and sanity test)

a3b1fb5

update ariba (and sanity test)

7993618

update kmerresistance (and sanity tests)

a668793

update resfinder (and sanity tests)

47b1922

update resfinder 4 (and sanity tests)

d8caa26

drop .py from software name

c1d2d4f

Update test_sanity.py

711f9cb

update RGI (and sanity tests)

1035acd

update srax (and sanity tests)

8c846a1

cimendes linked an issue May 16, 2022 that may be closed by this pull request

AMR Variant detection - Parsers to be updated #70

Closed

22 tasks

cimendes and others added 16 commits May 16, 2022 10:21

update groot (and sanity tests)

cedacb3

update deeparg

d6be340

update srst2

324f21d

start tbprofiler (not working)

5e6ee3d

Update StarAmrIO.py

e455be7

Update MykrobeIO.py

3e1805c

Update ResFamsIO.py

465b11e

Merge branch 'update_schema' into update_parsers

2f571f5

Add mutational parsing for AMRFinderPlus #70

fb977c2

Fix tests, deprecate resfinder <4, convert genetic_variation_type to …

4352585

…use constants

Add pointfinder parser and tests

c3713c9

Add RGI parsing for variants in main mode #70

c74a1b7

Add Ariba variant parsing for #70

bc81a3d

Add staramr variant and sanity #70

4c502a7

Add resfams sanity test

daee621

Remove extraneous print in Ariba

ad6f193

fmaguire marked this pull request as ready for review August 21, 2022 03:06

fmaguire merged commit 00176a9 into update_schema Aug 21, 2022

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