vcf-expression-annotator updates - #92
Merged
Merged
Conversation
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
updates the docs to reflect that it writes to the FORMAT field, not INFO
Right now, it's impossible to annotate two different samples in the same VCF with GX tags, as the tool will die when it encounters GX in the header. This fixes it with the following flags:
--forceallows the tool to proceed, even if it sees an existing GX flag--overwriteallows the tool to overwrite existing GX values. By default, it will only overwrite blank or absent values (same goes for the TX field on both of these). This is "safer" against unintended overwriting.adds tests of both of these params
updates docs with both of these params
Closes #82