Add optional Desc field to set the description in the header.

[roryk]

HI Brent,

This adds a Desc field to the annotation configuration so you can override what the description of the field is in the header. Go is new to me so let me know if I screwed anything up.

---

Note

Adds optional Desc to annotation config and sources, using it to override INFO header descriptions.

• API:
  • api.Source: add Desc field and use it in UpdateHeader to override auto-generated descriptions.
• Shared:
  • shared.Annotation: add Desc field and propagate it in Flatten to Source.

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[roryk]

The tests don't work for me-- I think there are some hard-coded paths in there, so I couldn't run them. I checked with and without the description though on my test file and it works ok.

[brentp]

I'm a little hesitant about this because I want to keep the .conf stuff as light as possible so that it's not intimidating to write (or to read the docs about it). Do you really need to customize the Description?

[roryk]

Hi @brentp,

Thanks for the response. I think maybe I'll end up editing it, to try to avoid fielding endless questions about what something like:

##INFO=<ID=possible_rnaedit,Number=0,Type=Flag,Description="calculated by lua:is_edit_flag(ref, alt) of overlapping values in column 4 from RADAR.bed.gz">

means. But I totally hear you about feature creep making stuff turn into a complicated mess. I can replace it after, it doesn't have to be something done in vcfanno for sure.

[brentp]

oh, I see. Let me think on it.

[brentp]

what about changing the description to something more generic like:

caclulated from overlapping values in columns 4 of RADAR.bed.gz

?
Instead of adding Desc to the config?

[roryk]

Hi Brent,

'calculated from overlapping values in columns 4' doesn't really describe how we got there though, since there is some other logic that went in it. For this example we did some checking if it was a SNP and if it was a valid edit event, etc. Maybe that is information handled better outside of the VCF file though, looking at the other INFO field descriptions they aren't too descriptive.

Thanks!

[hkeward]

+1 to being able to override the description in the config; I want to be able to add context about what that column actually contains. I will reheader after the fact, but it would be nice to be able to set descriptions directly through vcfanno.

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[cursor]

Bug: Description Interference with DP2 Type/Number Metadata

When s.Desc is set (not empty), the if-else chain will skip the DP2 field handling at lines 386-389, which not only sets the description but also critically sets number = "2" and ntype = "Integer". This means that if a user provides a custom description for a DP2 field, the VCF header will have incorrect type and number metadata. The logic for setting number and ntype should be separated from description generation so that custom descriptions don't bypass field-specific type/number settings.