Smarter unexpected sequence report #32
Merged
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
Rather than sample unexpected sequences by % of each column barcode's unexpected sequences, we set a maximum number of row barcodes for which we are willing to track unexpected sequences. When reading the unexpected sequence cache, we take 1 barcode from each shard in turn, until we have read all of them or established a sample of that size. All further unexpected sequences that are not found in that set are not tracked. This lets us bound the memory that PoolQ uses for its unexpected sequence reporting, without needing to individually track the sizes of individual shards. It should also perform better than the previous strategy since it reads the cache only once.
tmgreen
reviewed
Feb 13, 2024
src/main/scala/org/broadinstitute/gpp/poolq3/reports/UnexpectedSequenceWriter.scala
Show resolved
Hide resolved
tmgreen
reviewed
Feb 13, 2024
src/main/scala/org/broadinstitute/gpp/poolq3/reports/UnexpectedSequenceWriter.scala
Outdated
Show resolved
Hide resolved
tmgreen
reviewed
Feb 13, 2024
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Outdated suggestions cannot be applied.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.
Rather than sample unexpected sequences by % of each column barcode's
unexpected sequences, we set a maximum number of row barcodes for which
we are willing to track unexpected sequences. When reading the
unexpected sequence cache, we take 1 barcode from each shard in turn,
until we have read all of them or established a sample of that size. All
further unexpected sequences that are not found in that set are not
tracked.
This lets us bound the memory that PoolQ uses for its unexpected
sequence reporting, without needing to individually track the sizes of
individual shards. It should also perform better than the previous
strategy since it reads the cache only once.