minimap3 parallelism improvements #275
Closed
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
…ation errors in the `computeMap.hpp` file.
# for free
to join this conversation on GitHub.
Already have an account?
# 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Outdated suggestions cannot be applied.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.
The goal of this branch is to run minimap3 in a more parallel mode, particularly important when mapping a small number of contigs against each other. Parallelism is currently over query contig. This can be broken down much further, potentially over individual segments, although the final merging and filtering steps will remain single threaded per query sequence. An additional goal is to break the target index into chunks, so that we will be able to limit total memory usage. In this case as well we'll need to collect all
unfilteredMappingsfrom each subset of the full query/target comparison. I'm trying to work through the problem in small chunks without breaking the build or tests.