add /1 or /2 information back into read name if missing
#1
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
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Outdated suggestions cannot be applied.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.
cc @ctb:
This PR modifies
calc-coverage-diff-2.pyto add/1and/2read name suffixes back into each read name when missing. Read pair information is stored in the bamFLAGfield, which pysam interprets for us.When running
calc-coverage-diff-2.pypreviously, we were running into issues where we only had read pair information for some files. Upon digging, this may be because thebam2fqstep used ingenome-gristadds/1and/2information back into read names after it is presumably dropped in the minimap2 step.