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-sam-bam-basicsgit 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-sam-bam-basics)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-sam-bam-basics"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-sam-bam-basics/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-sam-bam-basics"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-sam-bam-basics.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 | $0.00045 | $0.04286 |
| Opus 5 | $0.00023 | $0.02143 |
| Sonnet 5 | $0.00009 | $0.00857 |
| Haiku 4.5 | $0.00005 | $0.00429 |
Grade A, and why
bio-sam-bam-basics 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 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.
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.
This is a copy
95% identical to bio-sam-bam-basics — 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 — 381 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.
SAM/BAM/CRAM Basics
"Read a BAM file" -> Open a binary alignment file and iterate over aligned reads with their mapping coordinates, flags, and quality scores.
- Python:
pysam.AlignmentFile()(pysam) - CLI:
samtools view(samtools) - R:
scanBam()(Rsamtools)
View and convert alignment files using samtools and pysam.
Format Overview
| Format | Description | Use Case |
|---|---|---|
| SAM | Text format, human-readable | Debugging, small files |
| BAM | Binary compressed SAM | Standard storage format |
| CRAM | Reference-based compression | Long-term archival, smaller than BAM |
SAM Format Structure
@HD VN:1.6 SO:coordinate
@SQ SN:chr1 LN:248956422
@RG ID:sample1 SM:sample1
@PG ID:bwa PN:bwa VN:0.7.17
read1 0 chr1 100 60 50M * 0 0 ACGT... FFFF... NM:i:0
Header lines start with @:
@HD- Header metadata (version, sort order)@SQ- Reference sequence dictionary@RG- Read group information@PG- Program used to create file
Alignment fields (tab-separated):
- QNAME - Read name
- FLAG - Bitwise flag
- RNAME - Reference name
- POS - 1-based position
- MAPQ - Mapping quality
- CIGAR - Alignment description
- RNEXT - Mate reference
- PNEXT - Mate position
- TLEN - Template length
- SEQ - Read sequence
- QUAL - Base qualities
- Optional tags (NM:i:0, MD:Z:50, etc.)
samtools view
View BAM as SAM
samtools view input.bam | head
View with Header
samtools view -h input.bam | head -100
What ships with it
3 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 · 381 lines · 45 tokens per session scan A 0571c866e062
bio-sam-bam-basics is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed today), licensed MIT. It adds 45 tokens to every session and 4,286 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-sam-bam-basics, differing in 12 lines, and is treated as a copy.
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