Fix percentage of ordered reads in QC-report

[talnor]

Description

The features of this PR primarily concerns end-users/bioinformaticians/internals

The percentage of ordered reads in the 'Antal Reads' column of the QC-report showed incorrect numbers. This was due to reads vs. read pairs confusion regarding the information in the apptags.

The percentage of ordered reads will now be divided by 2.

Primary function of PR

• [X] 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

This is a description of the tests necessary to verify the stability of the PR.

Basic test routine:

• _bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh pct_reads_fix_
• _Select installer options "S_microSALT" , "release" and "pct_readsfix"
• us
• _source activate S_microSALT_
• _export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json_
• microSALT analyse project MIC3109

Verify that the percentage of ordered reads is correct (i.e. equals the total reads / 610^6 100). Also verify that the code changes doesn't generate any unexpected error messages or graphical glitches in the report.

Test results

All percentages calculated correctly. See results below. No error messages or glitches to report.

Sign-offs

• [x] Code reviewed by @sylvinite
• [x] Code tested by @talnor
• [x] Approved to run at Clinical-Genomics by @ingkebil

[talnor]

MicroSALT QC-report results

Calculations:

[sylvinite]

Looks good. Since the value was merely aesthetic, no prior runs need to be re-done. Just make sure to deploy this after the routine samples for this week have been started.