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-filteringgit 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-filtering)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-filtering"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-filtering/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-filtering"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-filtering.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 | $0.00044 | $0.04369 |
| Opus 5 | $0.00022 | $0.02184 |
| Sonnet 5 | $0.00009 | $0.00874 |
| Haiku 4.5 | $0.00004 | $0.00437 |
Grade A, and why
bio-alignment-filtering 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 11d 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.
for read in infile.fetch(chrom, start, end): This is a copy
98% identical to bio-alignment-filtering — 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 — 419 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 Filtering
"Filter my BAM file to keep only high-quality reads" -> Select reads by FLAG bits, mapping quality, and genomic regions using samtools view or pysam.
- CLI:
samtools viewwith-F/-f/-q/-Lflags (samtools) - Python:
pysam.AlignmentFileiteration with attribute filters (pysam)
Filter alignments by flags, quality, and regions using samtools and pysam.
Filter Flags
| Option | Description |
|---|---|
-f FLAG |
Include reads with ALL bits set |
-F FLAG |
Exclude reads with ANY bits set |
-G FLAG |
Exclude reads with ALL bits set |
-q MAPQ |
Minimum mapping quality |
-L BED |
Include reads overlapping regions |
Common FLAG Values
| Flag | Hex | Meaning |
|---|---|---|
| 1 | 0x1 | Paired |
| 2 | 0x2 | Proper pair |
| 4 | 0x4 | Unmapped |
| 8 | 0x8 | Mate unmapped |
| 16 | 0x10 | Reverse strand |
| 32 | 0x20 | Mate reverse strand |
| 64 | 0x40 | First in pair (read1) |
| 128 | 0x80 | Second in pair (read2) |
| 256 | 0x100 | Secondary alignment |
| 512 | 0x200 | Failed QC |
| 1024 | 0x400 | Duplicate |
| 2048 | 0x800 | Supplementary |
Filter by FLAG
Keep Only Mapped Reads
samtools view -F 4 -o mapped.bam input.bam
Keep Only Unmapped Reads
samtools view -f 4 -o unmapped.bam input.bam
Keep Only Properly Paired
samtools view -f 2 -o proper.bam input.bam
Remove Duplicates
samtools view -F 1024 -o nodup.bam input.bam
Remove Secondary and Supplementary
samtools view -F 2304 -o primary.bam input.bam
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.
- 11d ago First seen · 419 lines · 44 tokens per session scan A 8f45310876e0
bio-alignment-filtering is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (403 stars, last pushed today), licensed MIT. It adds 44 tokens to every session and 4,369 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 98% identical to bio-alignment-filtering, differing in 12 lines, and is treated as a copy.
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