Add ID subfield to VCF v4.3 test file's structured header #773
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
In VCF v4.3 structured meta-information lines must have an ID subfield. Split the value into identifier-like ID and text Description subfields to demonstrate the structured benefit, though for a non-INFO/FORMAT/etc line there's probably nothing requiring ID's value to be identifier-like. Fixes samtools#772. This leaves the similar 4.1 and 4.2 files as is, as it is less clear whether ID-less structured headers are merely discouraged there.
jmarshall
force-pushed
the
example-structured-id
branch
from
15e6da4
to
5f49f9a
Compare
zaeleus
approved these changes
Jun 24, 2024
There was a problem hiding this comment.
The fix looks good to me.
This leaves the similar 4.1 and 4.2 files as is, as it is less clear whether ID-less structured headers are merely discouraged there and/or is unspecified and largely left up to implementations — cf #760.
It's not up to implementations if an authoritative example is expected to pass. Leaving them forces parsers to accept such header records, despite the behavior being undefined in those versions.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
In VCF v4.3 structured meta-information lines must have an ID subfield. Split the value into identifier-like ID and text Description subfields to demonstrate the structured benefit, though for a non-INFO/FORMAT/etc line there's probably nothing requiring ID's value to be identifier-like. Fixes #772.
This leaves the similar 4.1 and 4.2 files as is, as it is less clear whether ID-less structured headers are merely discouraged there and/or is unspecified and largely left up to implementations — cf #760.