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fix-ensure-all

Fix: ensure ALL documents use 'Pseudohomologous Region' for PHR

Metadata

Statusdone
Assignedagent-538
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-04-02T14:18:16.499332904+00:00
Started2026-04-02T14:18:36.889667342+00:00
Completed2026-04-02T14:24:44.200817994+00:00
Tagsfix,urgent, eval-scheduled
Eval score0.85
└ blocking impact0.95
└ completeness0.80
└ coordination overhead0.95
└ correctness0.95
└ downstream usability0.85
└ efficiency0.90
└ intent fidelity0.83
└ style adherence0.85

Description

CRITICAL CONTEXT

PHR = Pseudohomologous Region. This is the ONLY correct expansion. Read subtelomeric_analysis_report.md for authoritative usage.

PHRs are NOT:

  • Palindromic Heterochromatin Repeats (hallucinated)
  • Pericentromeric Homologous Regions (wrong)
  • Pericentromeric Highly Repetitive regions (wrong)
  • Subtelomeric Pericentromeric regions (wrong)

PHRs ARE: Pseudohomologous Regions — subtelomeric regions where non-homologous chromosomes share high-identity sequence (>95% identity) due to inter-chromosomal ectopic recombination/exchange.

Goal

Scan EVERY .md file in the working directory. For each file:

  1. Search for any expansion of PHR that is NOT 'Pseudohomologous Region'
  2. Search for 'pericentromeric', 'palindromic', 'heterochromatin repeat' in context of PHR
  3. Fix all instances to either use just 'PHR' (if context is clear) or 'Pseudohomologous Region (PHR)'
  4. Also check for any remaining biology errors while you're reading each file

Just fix the files. Don't write elaborate reports. Log which files were changed and which were clean.

Files to check

Run: find . -maxdepth 1 -name '*.md' and check every single one.

Validation

  • grep -ri 'palindromic' *.md returns nothing
  • grep -ri 'pericentromeric' *.md returns nothing (in context of PHR — pericentromeric is a real genomic term but should not be used to describe PHRs)
  • grep -ri 'heterochromatin repeat' *.md returns nothing in PHR context

Depends on

Required by

Log