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 PKU-YuanGroup/OpenAI4S --skill bio-alignment-files-alignment-indexinggit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-alignment-files-alignment-indexing)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-indexing"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-indexing/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-indexing"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-indexing.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00041 | $0.02878 |
| Opus 5 | $0.00020 | $0.01439 |
| Sonnet 5 | $0.00008 | $0.00576 |
| Haiku 4.5 | $0.00004 | $0.00288 |
Grade A, and why
bio-alignment-indexing scanned grade A with 1 finding 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 12d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
count = sum(1 for _ in bam.fetch(chrom, start, end)) This is a copy
95% identical to bio-alignment-indexing — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 320 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Alignment Indexing
Create indices for random access to alignment files using samtools and pysam.
"Index a BAM file" -> Create a .bai/.csi index enabling random access to genomic regions.
- CLI:
samtools index file.bam - Python:
pysam.index('file.bam')
Index Types
| Index | Extension | Max contig | Bin shift | When required |
|---|---|---|---|---|
| BAI | .bai / .bam.bai |
2^29 bp ≈ 537 Mbp | fixed (16 kb) | Default for human, mouse, fly, fish |
| CSI | .csi / .bam.csi |
2^(min_shift + depth*3) | configurable via -m |
Required for any contig >537 Mbp |
| CRAI | .crai / .cram.crai |
chunk-based | n/a | CRAM only |
| TBI | .tbi |
2^29-1 | fixed | tabix VCF/BED -- same limit as BAI |
Which Index for Which Genome
| Genome | Largest contig | Index |
|---|---|---|
| GRCh38 / GRCh37 (human) | 248 Mbp | BAI |
| GRCm39 (mouse) | 195 Mbp | BAI |
| GRCz11 (zebrafish), TAIR10 (Arabidopsis) | 78 Mbp / 30 Mbp | BAI |
| Wheat IWGSC (Triticum aestivum) | ~830 Mbp (chr3B) | CSI |
| Pine, fir, axolotl, sugar pine | multi-Gbp | CSI with larger -m |
| Long-read assembly with very large contigs | varies | check cut -f2 ref.fa.fai | sort -nr | head -1 |
For polyploid plants and salamander-scale genomes, increase the bin shift:
# Default CSI matches BAI bin layout: 2^(14 + 5*3) = 2^29 bp ≈ 537 Mbp per contig
samtools index -c file.bam
# Larger min_shift for contigs >537 Mbp (wheat, axolotl, sugar pine)
samtools index -c -m 18 file.bam # 2^(18+15) = 2^33 = ~8.5 Gbp per contig
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 12d ago First seen · 320 lines · 41 tokens per session scan A 1a0155e83a68
bio-alignment-indexing is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 41 tokens to every session and 2,878 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 95% identical to bio-alignment-indexing, differing in 12 lines, and is treated as a copy.
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