bio-alignment-sorting skillA
bio-alignment-sorting is agent-read markdown (skill) from pku-yuangroup/openai4s: Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis..
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 Sorting
Sort alignment files by coordinate or read name using samtools and pysam.
**"Sort a BAM file"** -> Reorder reads by genomic coordinate (for indexing/variant calling) or by name (for paired-end processing).
- CLI: `samtools sort -o sorted.bam input.bam`
- Python: `pysam.sort('-o', 'sorted.bam', 'input.bam')`
## Sort Orders
| Order | Flag | Use Case |
|-------|------|----------|
| Coordinate | default | Indexing, visualization, variant calling |
| Name | `-n` | Paired-end processing, fixmate, markdup |
| Tag | `-t TAG` | Sort by specific tag value |
## samtools sort
### Sort by Coordinate (Default)
```bash
samtools sort -o sorted.bam input.bam
```
### Sort by Read Name
```bash
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-sorting@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-sorting@sha256:5c61a3b7166c959aPin 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.
[](https://markdownregistry.com/a/art_q5kft7garayatrnp)
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Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_q5kft7garayatrnp GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-sorting GET https://markdownregistry.com/api/v1/blob/5c61a3b7166c959ae2eabad742edfdcef2a699d202635b5b3f7a9c373966c236
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