149 fix missing resistances

[samuell]

Description

Fixes #149 about missing OXA-48, sometimes being sometimes being reported as OXA-566 instead.

Primary function of PR

• Hotfix
• Patch
• Minor functionality improvement
• New type of analysis
• Backward-breaking functionality improvement
• This change requires internal documents to be updated
• This change requires another repository to be updated

Testing

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh BRANCHNAME
• us
• source activate S_microSALT
• (SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
• Select a relevant subset of the following:
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109
• microSALT analyse project ACC5551

Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

• Code tested by @octocat
• Approved to run at Clinical-Genomics by @sylvinite

[karlnyr]

Minor comments, nice 👍

[samuell]

Important clarification: This issue did not solve the reported missing VIM genes. See #180 for that one.

Initially we thought the fix would address both issues, but the VIM issue turned out to have different root cause, and was created as a separate issue #180

[samuell]

As can be seen here, OXA-48 turns up in the Typing report when run on MicroSALT 4.0.0, but did not before for the same sample, where instead OXA-566 showed up, for the same sample (Ending with A10), for case elegantflamingo.

MicroSALT 3.5.5, where you can see only OXA-566 being wrongly found:

MicroSALT 4.0.0, where you can see OXA-48 being correctly found: