Stop samtools cat from outputting multiple CRAM EOF markers. #1422
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
Samtools cat naively copies all incoming containers, and then writes an empty EOF container when closing the file. This leads to multiple internal EOF markers as they're implemented in CRAM as an empty container. Oddly there was code explicitly dealing with this, which seems redundant. Perhaps it served a purpose in early versions. Regardless internal EOF markers is permitted and are ignored, so this change is just for tidyness sake and to improve robustness incase bad implementations stop on the first EOF.
|
I am investigating some large memory allocations ~1 GB. It seems that a |
Amend previous commit following review comments. (As a distinct commit temporarily so the change we discussed is visible.) Empty containers still have a CRAM compression header block. So EOF blocks internal to a file need to have their block read even if we're not going to write it and the container back out again. This was visible by the following experiment. // Create a CRAM with internal EOF markers samtools-1.12 cat in.bam in.bam -o out1.bam // Concatenate such files together, with code prior to this commit samtools-previous-commit cat out1.bam out1.bam -o out2.bam
|
Merged into develop as 1ea60ad |
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Outdated suggestions cannot be applied.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.
Samtools cat naively copies all incoming containers, and then writes an empty EOF container when closing the file. This leads to multiple internal EOF markers as they're implemented in CRAM as an empty container.
Oddly there was code explicitly dealing with this, which seems redundant. Perhaps it served a purpose in early versions. Regardless internal EOF markers is permitted and are ignored, so this change is just for tidyness sake and to improve robustness incase bad implementations stop on the first EOF.