bio-sam-bam-basics SKILL.md skillA
bio-sam-bam-basics 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-sam-bam-basics@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-sam-bam-basics/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 14,978 bytes
- Repository stars
- 662
- License
- MIT
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
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. # 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 …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-sam-bam-basics@sha256:0571c866e0626ed5The 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_tatkqvsamm6f5gkf)
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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 zero-width or bidi control characters
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- pass: No link to an exfiltration or paste host
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- pass: No instruction to send local credentials anywhere
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- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
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- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_tatkqvsamm6f5gkf GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-sam-bam-basics GET https://markdownregistry.com/api/v1/blob/0571c866e0626ed5bcd336e9ff640f2962a996470c419822a0b256601fefb87e
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.