Update commands and VCF specification - Githubissues

maize-genetics / phg_v2

Practical Haplotype Graph (PHG) version 2

https://phg.maizegenetics.net/

Apache License 2.0

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Update commands and VCF specification #251

Closed btmonier closed 1 week ago

btmonier commented 1 week ago

Description

Updates the "Convenience Commands" documentation
- Adds new "summary stats" commands made by @tcasstevens and @lynnjo
- Adds new navigable section header
Updates VCF specifications to match current v2.4 specs, specifically with the ##ALT header section.

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

[ ] CHANGE (fix or feature that would cause existing functionality to not work as expected)
[ ] FEATURE (non-breaking change which adds functionality)
[ ] BUGFIX (non-breaking change which fixes an issue)
[ ] ENHANCEMENT (non-breaking change which improves existing functionality)
[x] NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

[ ] I have performed a self-review of my code
[ ] I have commented my code, particularly in hard-to-understand areas
[x] I have updated relevant documentation

Changelog entry

Please add a one-line changelog entry below. This will be copied to the changelog file during the release process.