Skip to content

perf(bam): parallel BGZF and record encoding (draft: measured slower, investigating) #164

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
BenjaminDEMAILLE wants to merge 1 commit into from
Closed

perf(bam): parallel BGZF and record encoding (draft: measured slower, investigating) #164

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 12 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,18 @@ Sections commonly used: Features, Bug fixes, Other changes.

## [Unreleased]

### Other changes

- BAM output now compresses and encodes on the rayon pool sized by
`--runThreadN`, instead of deflating one BGZF block at a time on the
writing thread. Output is unchanged: the multithreaded BGZF writer
stages into the same buffer size, emits through the same frame writer
and appends the same EOF block, and record encoding is split into
sub-ranges whose concatenation in input order is the serial stream.
Pinned by `multithreaded_bgzf_is_byte_identical_to_the_serial_writer`,
`parallel_encoding_is_byte_identical_at_every_worker_count` and
`bam_file_is_byte_identical_to_the_serial_path`.

### Features

- **STARsolo single-cell quantification (`--soloType`)** — the 10x
Expand Down
Loading
Loading