FixDataset Deep Dive

This chapter covers mutation policy and branch-safe application patterns.

FixDataset as layered transformation

A practical order for understanding behavior:

  1. flag normalization (-sys, -group, -pta),

  2. overlap/relabel policy application,

  3. jump insertion/pruning,

  4. par default enforcement,

  5. variant generation,

  6. optional QC-based apply actions.

Policy boundaries

Use catalogs for static mappings/tables and rules for strategy decisions:

  • catalogs: configs/catalogs/*

  • rules: configs/rules/*

Non-destructive first

Recommended default apply policy is comment-first:

  • fix_qc_action = "comment"

Only enable deletion after reviewing QC summaries and action lists.

Branch safety pattern

Use branch chaining:

  • base branch = previously validated stage,

  • new branch per mutation pass,

  • commit message documents the policy pass applied.

Variant generation

FixDataset can generate:

  • multiple include files: J*_all.<variant>.tim

  • variant par products (when configured)

Ensure classification + variant catalogs are both set and compatible.

Debug order for missing expected outputs

  1. verify stage toggles,

  2. verify branch/apply controls,

  3. verify catalog/rule file paths,

  4. verify output placement in pulsar and run result trees.

See also