+ document how to run bcftools commands from pysam #1275
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- this wasn't explicitly stated in the documentation. I was
using the notes described in [github issue 958][0] as a guide.
- in the changes also put updated links to the bcftools and htslib.org pages
[0]: pysam-developers#958
jmarshall
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Jan 21, 2025
…tation Describe both samtools and bcftools invocations. Supersedes #1275. Add reference documentation covering all the keyword arguments, etc. Describe in detail how to redirect output to a file, a common use case. Fixes #1096, fixes #1241, fixes #1323, et al. Update doc/conf.py's rst_epilog samtools and bcftools URLs to point to version-specific man pages, and have devtools/import.py update the URLs.
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Thanks for the suggestion to document the bcftools subcommands too. I've taken an alternative approach in 51ff3f1 and incorporated bcftools into the existing samtools documentation. |
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I recently had trouble running the
bcftoolscommands within pysam. I saw the "Using samtools commands within python" section within the documentation and thought things would behave similarly. I didn't find it to be true. I ended up finding the solution through github issue 958.I thought it would be nice to have this
bcftoolsfeature more explicitly documented for future users.Let me know if any additional changes are desired.