bio-sam-bam-basics skillA
bio-sam-bam-basics is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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. # 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 …
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How to install
mdr add pku-yuangroup/openai4s/bio-sam-bam-basics@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-sam-bam-basics@sha256:0571c866e0626ed5Pin 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_tatkqvsamm6f5gkf)
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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_tatkqvsamm6f5gkf GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-sam-bam-basics GET https://markdownregistry.com/api/v1/blob/0571c866e0626ed5bcd336e9ff640f2962a996470c419822a0b256601fefb87e
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