step-1-extract-chm13

Metadata

Status	done
Assigned	`agent-13`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-03-31T21:03:24.721336362+00:00
Started	2026-03-31T21:07:09.180844815+00:00
Completed	2026-03-31T21:08:24.263183727+00:00
Tags	`impl`, `eval-scheduled`
Eval score	0.84
└ blocking impact	0.95
└ completeness	1.00
└ coordination overhead	0.95
└ correctness	0.98
└ downstream usability	0.93
└ efficiency	0.95
└ intent fidelity	0.66
└ style adherence	0.92

Description

Goal

Create a clean BED file of CHM13 PHR intervals by extracting CHM13 rows from CHM13-HG002.sub-telo-phrs.bed and stripping PanSN prefixes.

Approach

grep '^CHM13#0#' CHM13-HG002.sub-telo-phrs.bed \
  | sed 's/CHM13#0#//' \
  > chm13.phrs.bed

Context

Check the research task output first for file locations and any caveats
Should produce ~37 intervals covering 41 chromosome arms
The BED columns are: chr, start, end, comma-separated list of chromosomes sharing sequence

Validation

chm13.phrs.bed exists and has ~37 lines
Chromosome names are standard (chr1, chr2, ...) without PanSN prefix
File is valid BED format (tab-separated, start < end)
Log the line count and first few lines

## Goal
Create a clean BED file of CHM13 PHR intervals by extracting CHM13 rows from `CHM13-HG002.sub-telo-phrs.bed` and stripping PanSN prefixes.

## Approach
```bash
grep '^CHM13#0#' CHM13-HG002.sub-telo-phrs.bed \
  | sed 's/CHM13#0#//' \
  > chm13.phrs.bed
```

## Context
- Check the research task output first for file locations and any caveats
- Should produce ~37 intervals covering 41 chromosome arms
- The BED columns are: chr, start, end, comma-separated list of chromosomes sharing sequence

## Validation
- `chm13.phrs.bed` exists and has ~37 lines
- Chromosome names are standard (chr1, chr2, ...) without PanSN prefix
- File is valid BED format (tab-separated, start < end)
- Log the line count and first few lines

Depends on

Required by

done step-2-intersect-genes

Log

2026-03-31T21:03:24.720299032+00:00 Task paused
2026-03-31T21:04:09.339180867+00:00 Task published
2026-03-31T21:07:09.180846508+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-03-31T21:07:23.704908155+00:00 Starting implementation: extracting CHM13 PHR BED intervals
2026-03-31T21:07:33.302746527+00:00 Reviewed research inventory - confirmed input file location and approach
2026-03-31T21:07:40.305025720+00:00 Examined input file format - proceeding with extraction
2026-03-31T21:07:47.543243805+00:00 Completed extraction - validating output
2026-03-31T21:08:09.894799313+00:00 Validated: chm13.phrs.bed exists with 37 lines, standard chromosome names (chr1, chr2, etc), valid BED format (tab-separated, start < end)
2026-03-31T21:08:16.330826762+00:00 Line count: 37, First line: chr1 2706 297706 (294Kb PHR), Successfully extracted and validated CHM13 PHR intervals
2026-03-31T21:08:24.263188075+00:00 Task marked as done
2026-03-31T21:09:07.835918384+00:00 FLIP score 0.66 below threshold 0.70 — triggering Opus verification