Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add HolobiomicsLab/asb-skill-collections --skill bedgraph-file-exportgit clone --depth 1 https://github.com/HolobiomicsLab/asb-skill-collectionsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/bedgraph-file-export)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/bedgraph-file-export"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/bedgraph-file-export.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00070 | $0.01424 |
| Opus 5 | $0.00035 | $0.00712 |
| Sonnet 5 | $0.00014 | $0.00285 |
| Haiku 4.5 | $0.00007 | $0.00142 |
Grade A, and why
bedgraph-file-export scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 98 lines — stays where its author put it; the contents beside it link to each section on GitHub.
bedgraph-file-export
Summary
Export per-bin sequencing depth (coverage) computed from cooler Hi-C files to bedGraph or tabular (CSV/TSV) format for downstream visualization and analysis. This skill bridges in-memory coverage track objects to portable, coordinate-annotated text formats.
When to use
After computing per-bin coverage depth using cooltools.coverage() on a loaded cooler object, when you need to (1) share the coverage track with non-Python tools, (2) visualize it in a genome browser, or (3) integrate it with downstream analyses that expect bedGraph or tabular input. Use this when your analysis requires bin coordinates alongside coverage values in a human-readable or browser-compatible format.
When NOT to use
- Input is already a bedGraph or coordinate-annotated tabular file; use direct format conversion instead.
- Coverage has not been computed or cooler object is not loaded; compute coverage first using cooltools.coverage().
- Analysis requires in-memory array operations or sparse matrix format; keep coverage as a Python object rather than exporting to disk.
Inputs
- cooler file (.cool or .mcool HDF5 format)
- coverage track object (output from cooltools.coverage())
- bin table with genomic coordinates (chrom, start, end)
Outputs
- bedGraph file (4-column: chrom, start, end, coverage)
- CSV or TSV table with bin coordinates and coverage values
How to apply
Following cooltools.coverage() computation, the resulting coverage track object contains per-bin sequencing depth values indexed by bin coordinates. Export this to bedGraph format (with columns: chromosome, start, end, coverage value) or tabular format (CSV/TSV with bin metadata and coverage) by iterating over bins, retrieving their genomic coordinates from the cooler file's bin table, pairing them with coverage values, and writing to file. Validate the output by checking (a) row count matches the number of bins in the cooler, (b) coordinate ranges are contiguous and non-overlapping, and (c) coverage values are numeric and within expected range (non-negative, typically matching total contact counts per bin).
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 98 lines · 70 tokens per session scan A 3dde4140166b
bedgraph-file-export is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 2d ago), licensed Apache-2.0. It adds 70 tokens to every session and 1,424 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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