bio-bam-statistics skillA
bio-bam-statistics is agent-read markdown (skill) from pku-yuangroup/openai4s: Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports..
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. # BAM Statistics **"Get alignment statistics and coverage from my BAM file"** -> Generate read counts, mapping rates, per-chromosome statistics, depth profiles, and coverage summaries. - CLI: `samtools flagstat`, `samtools stats`, `samtools depth`, `samtools coverage` (samtools) - Python: `pysam.AlignmentFile` with `pileup()` and `get_index_statistics()` (pysam) Generate alignment statistics using samtools and pysam. ## Quick Summary Commands | Question | Best tool | Why | |----------|-----------|-----| | Quick read counts by FLAG category | `samtools flagstat` | Fast; counts secondary+supp in totals | | Per-chromosome counts | `samtools idxstats` | Fast (needs index); **counts secondary+supp** | …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-bam-statistics@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-bam-statistics@sha256:15655223371768a9Pin 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_sardn3brxxsarzhp)
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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_sardn3brxxsarzhp GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-bam-statistics GET https://markdownregistry.com/api/v1/blob/15655223371768a9af117a854a477f49fdf2c6e3a2450ac879a83414a404dbe1
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