pysam SKILL.md skillA
pysam from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/pysam@v2.3Pins v2.3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/pysam/SKILL.md- Versions recorded
- 7
- Latest version
- v2.3, committed Oct 1, 2026
- First version recorded
- May 27, 2026
- Size
- 13,610 bytes
- Repository stars
- 56,497
- License
- MIT
Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
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
# pysam ## Overview Use pysam for low-level, streaming access to HTSlib-supported genomic formats: - `AlignmentFile` and `AlignedSegment` for SAM/BAM/CRAM - `VariantFile`, `VariantHeader`, and `VariantRecord` for VCF/BCF - `FastaFile` for indexed FASTA and `FastxFile` for sequential FASTA/FASTQ - `TabixFile` for BGZF-compressed, tabix-indexed BED/GFF/GTF/custom tables - `pysam.samtools` and `pysam.bcftools` for wrapped command dispatchers Current upstream baseline: **pysam 0.24.1** (7 September 2026), wrapping HTSlib/samtools/bcftools 1.24. Read `references/sources.md` before updating version-specific guidance. ## Installation Use the pinned release for reproducible work: ```bash uv pip install "pysam==0.24.1" ``` Confirm the runtime: ```python import pysam print(pysam.__version__) # 0.24.1 print(pysam.__samtools_version__) # 1.24 ``` Prebuilt wheels are available for supported macOS and Linux platforms. A source build needs a C compiler and HTSlib build dependencies; read the official installation guide linked from `references/sources.md`. ## First Decide Before writing code: 1. Identify the real format, compression, sort order, and available index. …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/pysam@sha256:afc275bbeb084553The line at the top of this page pins the label v2.3, 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_xsfrngazq7wc2ffi)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 7 versions of this file, between May 27, 2026 and Oct 1, 2026, about one every 21 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v2.3 latest | 2026-10-01 | a92663a | 13,610 B | A | view · diff |
| v2.2 | 2026-09-30 | ce9e6e9 | 12,884 B | A | view · diff |
| v2.1 | 2026-09-02 | 1e5eeff | 12,545 B | A | view · diff |
| v2.0 | 2026-07-26 | b085e11 | 11,587 B | A | view · diff |
| v2.0 | 2026-07-23 | 53c5897 | 11,590 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 10,015 B | A | view · diff |
| v1.0 | 2026-05-27 | 0936740 | 10,010 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (13610 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- 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
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_xsfrngazq7wc2ffi GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/pysam GET https://markdownregistry.com/api/v1/blob/afc275bbeb084553cd6507c4ffee848c46bef94dcd24c3b8a58d8b14d021ea09
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.