Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2 #18
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
…out 0x2, 0x8, 0x20, 0x40 and 0x80"
|
This has now been tested on UK10K cohort BAMs and in combination with a correction to samtools fixmates has resolved the problem we had with orphaned paired reads (which had run out of sync and were thus mismapping). |
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Outdated suggestions cannot be applied.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.
This patch fixes bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2. According to the spec "If 0x1 is unset, no assumptions can be made about... 0x2, 0x8, 0x20, 0x40 and 0x80".