Bugfix/specify lane ordinal sorting #46
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
When subsetting to a specific lane, the reads were being written to the wrong output file. This was caused by the list of samples internally not being in ascending order by ordinal, but the writers created after sorting the samples by ordinal. The fix is to order the samples by ordinal prior to creating the writers, and adding in validation code to ensure the samples are sorted in ascending order by ordinal. Also changed the ordinal of the undetermined sample to be one larger than the largest ordinal in the existing samples.
tfenne
approved these changes
Apr 28, 2023
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Outdated suggestions cannot be applied.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.
[bugfix] reads were written to the wrong file when --lanes was used
When subsetting to a specific lane, the reads were being written to the
wrong output file. This was caused by the list of samples internally
not being in ascending order by ordinal, but the writers created after
sorting the samples by ordinal.
The fix is to order the samples by ordinal prior to creating the
writers, and adding in validation code to ensure the samples are sorted
in ascending order by ordinal.
Also changed the ordinal of the undetermined sample to be one larger
than the largest ordinal in the existing samples.