Dev gcgi 1481 raw coverage autofill #504
Merged
+58
−28
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
iainrb
reviewed
Dec 19, 2024
added 2 commits
January 7, 2025 15:57
iainrb
requested changes
Jan 7, 2025
| # Check if coverage values are unique | ||
| coverage = filtered_data[columns_of_interest.MeanBaitCoverage].unique() | ||
| if len(coverage) != 1: | ||
| msg = f"Multiple coverage values found for group_id {group_id}: {coverage}." |
There was a problem hiding this comment.
Please log the error with self.logger.error(msg) before calling raise
| selected_value = coverage[0] | ||
| qc_dict[constants.RAW_COVERAGE] = int(round(selected_value, 0)) | ||
| else: | ||
| msg = f"No valid QC metrics found for group_id {group_id} after filtering out the normal." |
There was a problem hiding this comment.
Please log the error with self.logger.error(msg) before calling raise
| @@ -125,22 +150,22 @@ def render(self, data): | |||
| def process_ichor_json(self, ichor_metrics): | |||
| with open(ichor_metrics, 'r') as ichor_results: | |||
| ichor_json = json.load(ichor_results) | |||
| return(ichor_json) | |||
| return (ichor_json) | |||
There was a problem hiding this comment.
No parentheses needed here -- return ichor_json works and is simpler
| header_line = False | ||
| else: | ||
| next | ||
| return(int(round(unique_coverage, 0))) | ||
| return (int(round(unique_coverage, 0))) |
There was a problem hiding this comment.
Again, outermost parentheses are not needed -- can have return int(round(unique_coverage, 0))
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Outdated suggestions cannot be applied.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.
No description provided.