[query] Set QUAL to missing when it's "."#14697
Merged
Merged
Conversation
When we switched from using htsjdk to do most of our VCF parsing to using our own parser, we kept the behavior of setting missing QUAL to a sentinel value. This isn't necessary (or correct) for hail to do. The type of QUAL is optional float64 and we should preserve the missing value. Technically speaking this represents a backwards compatibility change. However, I think this is a bug in my attempt in the past to keep bug-for-bug compatibility with htsjdk rather than parsing the value into what people would expect.
patrick-schultz
approved these changes
Sep 20, 2024
patrick-schultz
left a comment
patrick-schultz
left a comment
Member
There was a problem hiding this comment.
Clearly the right behavior.
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
When we switched from using htsjdk to do most of our VCF parsing to using our own parser, we kept the behavior of setting missing QUAL to a sentinel value. This isn't necessary (or correct) for hail to do. The type of QUAL is optional float64 and we should preserve the missing value.
Technically speaking this represents a backwards compatibility change. However, I think this is a bug in my attempt in the past to keep bug-for-bug compatibility with htsjdk rather than parsing the value into what people would expect.