bio-alignment-indexing SKILL.md skillA
bio-alignment-indexing from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-alignment-indexing@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-alignment-files-alignment-indexing/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 9,961 bytes
- Repository stars
- 662
- License
- MIT
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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>` then `help(module.function)` to check signatures
- CLI: `<tool> --version` then `<tool> --help` to 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 |
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-indexing@sha256:1a0155e83a68c52dThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_cdkmxk3dld5gkcqw)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: No instruction to send local credentials anywhere
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_cdkmxk3dld5gkcqw GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-indexing GET https://markdownregistry.com/api/v1/blob/1a0155e83a68c52d593ba3de7f66e9a993f67bc47cce718832a7adca1bd44368
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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