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fix-executive-summary

Fix EXECUTIVE_SUMMARY.md tables: use community key instead of chromosome lists

Metadata

Statusdone
Assignedagent-579
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-04-02T21:45:25.389145853+00:00
Started2026-04-02T21:45:48.563886818+00:00
Completed2026-04-02T21:48:17.501739683+00:00
Tagsfix,formatting, eval-scheduled
Eval score0.72
└ blocking impact0.80
└ completeness0.65
└ coordination overhead0.95
└ correctness0.70
└ downstream usability0.75
└ efficiency0.85
└ intent fidelity0.84
└ style adherence0.80

Description

CRITICAL CONTEXT

PHR = Pseudohomologous Region.

Goal

Edit EXECUTIVE_SUMMARY.md to fix the gene family catalog table. Currently the table has incredibly long lines because each row lists all chromosome arms (e.g. 'chr1p, chr2p, chr3p, chr5p, chr6p, chr7p, chr8p, chr9p, chr11p, chr12p, chr15p, chr16p, chr17p, chr19p, chr20p, chrXp, chrYp'). This makes the table unreadable.

Fix

  1. Add a Community Key / Legend before the table. Something like:
### Leiden Community Key
| Community | Arms | Description |
|-----------|------|-------------|
| C1 | chr4q, chr10q + 16 others | D4Z4 macrosatellite sharing |
| C2 | chr3p, chr4p, chr9p, chr10p, chr16p, chr18p | Recurrent transfer pair |
| C3 | chr3q, chr7p, chr9q, chr11p, chr16q, chr19p | Largest community, f7501 sites |
| C5 | chr20q + others | Shared duplicon modules |
| C6 | chr17q + acrocentric q-arms | Mixed acrocentric/autosomal |
| C9 | chr16p (singleton) | AFR-enriched |
| C11 | chr1p, chr5q, chr6q, chr8p | OR4F21 sharing |
| C12 | chr2q, chr20p | Variable f7501 pair |
| C14 | chrXq, chrYq | PAR2 sharing |

Get the actual community definitions from enriched_genes_per_arm.md and enriched_genes_detailed_map.csv.

  1. Replace chromosome lists in the table with just the community ID(s). So instead of:

| WASHC1 | 16 | chr1p, chr2p, chr3p, chr5p, chr6p, chr7p, chr8p, chr9p, chr11p, chr12p, chr15p, chr16p, chr19p, chr20p, chrXp, chrYp | ... |

Use:

| WASHC1 | 16 | 16 p-arms | C3, C11, C12, C14 | ... |

  1. Keep copy counts and arm counts as numbers, just replace the full chromosome lists with community references.

  2. Don't change anything else in the document — just fix the table formatting.

Validation

  • No table row exceeds ~120 characters
  • Community key is present and correct
  • All gene families still have their copy counts and community assignments
  • The document is readable in a normal terminal/editor without horizontal scrolling

Depends on

Required by

Log