Fix bug in ClusterBatch when SR2POS not present #775
Merged
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
mwalker174
reviewed
Feb 7, 2025
| @@ -153,7 +153,7 @@ def convert(record: pysam.VariantRecord, | |||
| new_record.info['STRANDS'] = '+-' | |||
| # END information is lost when setting POS=END, so we need to set it to SR2POS if it's available | |||
| # Note that the END position is only important following SR breakpoint refinement in FilterBatch | |||
| if record.info.get('SR2POS') is not None: | |||
| if 'SR2POS' in record.info: | |||
There was a problem hiding this comment.
Suggested change
| if 'SR2POS' in record.info: | |
| if 'SR2POS' in record.info and record.info['SR2POS'] is not None: |
I would check for both that the key doesn't exist but also if the key exists and the value is not null to be safe
|
Did you test this on CombineBatches as well? |
|
@mwalker174 Updated with your suggestion and retested ClusterBatch & CombineBatches with the new docker |
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Outdated suggestions cannot be applied.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.
With the latest version, ClusterBatch failed during GatkToSvtkVcf due to SR2POS being missing. This PR updates the check to one that does not fail if SR2POS is not in the header. Tested on a clone of the joint-calling workspace with an updated docker and the same inputs that failed before.