Remove redundant BAM file open in paired mode #32
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
Opening a BAM file is an expensive operation as the index needs to be fully read. In paired reads mode, at every contig change, the file was being opened again to iterate over all reads from the previous contig. This is usually not an issue for genome alignments, but transcriptome alignments may have ~100k contigs, which makes this an expensive operation. Ideally, the two-pass mode should not have to read the file again, and instead just maintain a rolling window of reads in memory.
|
With this change, the test case in the linked issue takes 14 minutes now instead of 6.3 hours. |
|
@Daniel-Liu-c0deb0t Can you please accept this PR? |
|
I just wanted to express explicit support for this proposal! While I am not familiar with the implementation details, I think, it is a very important fix. Transcriptomic alignments or draft genome assemblies typically have numerous contigs and if this fix streamlines the deduplication of those input files so dramatically, I would love to see it merged! |
11 tasks
1 task
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Outdated suggestions cannot be applied.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.
Fixes #31.
Opening a BAM file is an expensive operation as the index needs to be
fully read. In paired reads mode, at every contig change, the file was
being opened again to iterate over all reads from the previous contig.
This is usually not an issue for genome alignments, but transcriptome
alignments may have ~100k contigs, which makes this an expensive
operation.
Ideally, the two-pass mode should not have to read the file again, and
instead just maintain a rolling window of reads in memory.