Skip to content

feat: output anndata - #237

Draft
ilan-gold wants to merge 4 commits into
mainfrom
ig/anndata
Draft

feat: output anndata#237
ilan-gold wants to merge 4 commits into
mainfrom
ig/anndata

Conversation

@ilan-gold

@ilan-gold ilan-gold commented Aug 25, 2026

Copy link
Copy Markdown

Fixes #1

See #1 (comment) for the plan / approach.

Currently dependent on the bug highlighted in scverse/anndata-rs#44 which may not be a bug but instead something that should be changed in python.

Todos:

  • Resolve the obsm dataframe mess
  • Clean up some of the AI output
  • Relatedly, decide on how extras should be structured
  • Check speed

@BenjaminDEMAILLE

Copy link
Copy Markdown
Contributor

Heads-up on the conflict state, from a pass over the whole PR queue.

Two of the three conflicts against current main are mechanical and I verified a resolution locally:

  • src/solo/mod.rs: pub mod adata; and pub mod cell_reads; are both additions, so both stay.
  • src/junction/sj_output.rs: main still inlines the surviving-junction filter and sort inside write_sj_lines, while this branch factored the same logic into sorted_junctions(params). The helper is equivalent (same filter, same sort key), so this branch's version wins and main's inline block goes.

The third is not mechanical and is yours to decide: src/solo/count.rs has two ~110-line hunks where this branch rewrote the matrix writer to take a cells slice, and main reworked the same function's record folding (1MM_multi resolution off exact_count_snapshot, std::mem::take of the recorder). Picking one shape over the other changes what the anndata writer receives, so I left it alone rather than guessing.

No commits were pushed to this branch.

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.

Output anndata files

2 participants