Skip to content

Expose BGEN tuning options#32

Merged
jeromekelleher merged 3 commits into
sgkit-dev:mainfrom
jeromekelleher:new-bgen-code
May 19, 2026
Merged

Expose BGEN tuning options#32
jeromekelleher merged 3 commits into
sgkit-dev:mainfrom
jeromekelleher:new-bgen-code

Conversation

@jeromekelleher
Copy link
Copy Markdown
Member

No description provided.

vcztools.BgenEncoder accepts total_string_length and pad_byte but
ViewBgenOptions does not yet surface them. Add a temporary
biofuse/_vcztools_compat.py shim that subclasses ViewBgenOptions to
add the two fields, layers --total-string-length and --pad-byte
onto the existing decorator, and extends from_click_kwargs to read
them. _bgen_encoder_factory passes the new fields straight to
BgenEncoder; nothing else in cli.py / encoder_host.py changes.

Delete the shim (and the TestViewBgenOptionsShim class) once the
fields land in vcztools upstream.
The --total-string-length and --pad-byte options have landed in
vcztools.ViewBgenOptions, so the biofuse-local monkeypatch is no
longer needed. Bumps the vcztools lock past commit a8ce91d and
loosens the non-ASCII pad-byte CLI test to match upstream's strict
encoder, which raises UnicodeEncodeError instead of BadParameter.
@jeromekelleher jeromekelleher merged commit 698b6c8 into sgkit-dev:main May 19, 2026
5 checks passed
@jeromekelleher jeromekelleher deleted the new-bgen-code branch May 19, 2026 11:03
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant