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Resolve "Trio filtering not available when CNV and SNVs combined"

Øyvind Evju requested to merge 1975-trio-filtering-not-available-when-cnv-and-snvs-combined into dev

Description

When an analysis consists of a trio (samples: proband, mother, father), in addition to a separate proband-sample (in this case, a CNV sample), the logic for selecting Trio-filtering failed. Fix added to check that if an analysis contains a trio, then trio-filtering is available.

This created some further problems in the SegregationFilter. When it is provided with the allele ids for the analysis, it will try to do segregation filtering on all of them. However, this includes allele_ids for the sample without family information, and fails.

Fix is added to identify subset of allele ids in the family, and run segregation filter on these, and never filter the other allele ids (segregation_not_applicable).

Related issues

Notes to review (code/docs/QA)

Tests

General

  • Tests have been added that prove my fix is effective or that my feature works
  • Related tests have been modified/removed

Hypothesis testing:

  • Soak testing has been done
  • Distribution between positive / negative cases has been checked

Database

  • Includes changes to database schema
  • Includes necessary database migrations

Configuration

  • Includes changes to configuration
  • Includes configuration migration instructions in documentation

Closes #1975 (closed)

Edited by Øyvind Evju

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