PacBio - implement parsing of failed reads metrics

[diitaz93]

Description

Closes https://github.com/Clinical-Genomics/add-new-tech/issues/64
The read metrics we parsed came from a file containing only HiFi data. It is important to parse the failed read metrics too. There is a file containing both HiFi and failed metrics (m84202_240522_135641_s1.ccs_report.json). It is, however, generated by another software so the values are not exactly the same as the metrics parsed before. @J35P312 assured that the difference was negligible.

Added

• New parameters to parse from ccs file:
  • <Q20 Reads
  • <Q20 Yield (bp)
  • <Q20 Read Length (mean, bp)

Changed

• Renamed HiFiMetrics model to ReadMetrics
• The path to the ccs file

Fixed

• Removed old ccs file usage and fixture

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[ChrOertlin]

Nice!