bio-alignment-indexing skillA
bio-alignment-indexing is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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 |
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-indexing@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-indexing@sha256:1a0155e83a68c52dPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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