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CellRanger-compatible `outs/` output (`metrics_summary.csv`, `.h5` matrices, `web_summary.html`) — checking the development method before opening PRs

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メンテナーはふだん 4 日以内に返信

@Psy-Fer がすでに取り組んでいます。

2026年10月28日 から。

評価

難易度
5/5
見積もり時間
1週間以上
初心者へのやさしさ
20/100
issue の種類
機能追加
明瞭さ
明確に書かれている
活発さ
活発
技術スタック
rust
領域
backend, data

調査の方向性

Start by reading CONTRIBUTING's policy on compatibility work and review the proposed three PR themes: metrics and gzipped matrices, HDF5 matrices, and the HTML report. The issue names no repository files or tests to run. Done means maintainers decide whether the observed-output method is acceptable, whether the output belongs in this project, and whether the proposed split is right.

索引モデルが issue の本文から書いたものです。

説明

sensitive license

CONTRIBUTING says a contribution that reproduces the behaviour of a tool under a
sensitive licence needs to be discussed and agreed before work starts. I have
written this code already, which is my mistake — I am raising it now rather than
opening the PRs, and I will drop the work if the answer is no.

What I would like agreed is the method, which I believe is the one the policy
describes as acceptable, and then whether the result is wanted at all.

What it does

An opt-in flag (--soloCellRangerOuts Yes, off by default, no effect on any
existing output) that writes, beside Solo.out/:

outs/metrics_summary.csv
outs/raw_feature_bc_matrix/{barcodes,features}.tsv.gz, matrix.mtx.gz
outs/filtered_feature_bc_matrix/{barcodes,features}.tsv.gz, matrix.mtx.gz
outs/raw_feature_bc_matrix.h5
outs/filtered_feature_bc_matrix.h5
outs/web_summary.html

The point is that an existing pipeline that reads outs/filtered_feature_bc_matrix.h5
keeps working. Solo.out/ is never altered.

How it was developed — this is the part I want checked

Entirely from observed outputs, which CONTRIBUTING lists as an acceptable
method ("from public documentation, published papers, or observed inputs and
outputs"):

  • The field names, their order, and the number formatting in
    metrics_summary.csv were read from two real CellRanger output files
    (one 8.0.1, one 10.0.0).
  • The HDF5 layout was read from real .h5 outputs with h5py — group and
    dataset names, dtypes, the CSC convention, and the root attributes.
  • The -1 GEM-group barcode suffix was read from real barcodes.tsv.gz.

No CellRanger source was read, ported or paraphrased, by me or by any tool.
In particular I deliberately did not open the JavaScript bundle inside a real
web_summary.html; the page in this work is laid out and drawn from scratch and
is not intended to resemble CellRanger's report. The only thing taken from their
side of web_summary.html is the set of metric names, which are the same ones
already in metrics_summary.csv.

What is and is not claimed

Every figure is rustar-aligner's own. The names are CellRanger's so that
existing parsers keep working; the definitions are not claimed to equal
CellRanger's, and this is stated in DIVERGENCE.md and in the generated page
itself. Two concrete examples of the difference, measured on the same 10M reads:

  • Reads Mapped Confidently to Genome: rustar-aligner reports STAR's uniquely
    mapped fraction (75.1%, against STARsolo's 75.3% on the same reads).
    CellRanger reports 80.8% for the same-named field, so it means something else.
  • Mean Reads per Cell: CellRanger divides all reads by the cell count;
    STAR's Summary.csv divides reads in called cells by it
    (meanReadPerCellUnique = nReadInCellsUnique / nCells,
    SoloFeature_cellFiltering.cpp). The CellRanger-named file uses CellRanger's
    definition; Summary.csv keeps STAR's.
Questions
  1. Is the observed-outputs method acceptable here, given it happened before this
    discussion rather than after?
  2. If so, is this output wanted in rustar-aligner at all, or is it better as a
    separate tool?
  3. If wanted, is the split below right? Each is independently useful and I would
    open them in order.
Proposed PRs
Theme
1 --soloCellRangerOuts: metrics_summary.csv + the gzipped matrix mirror
2 the two .h5 matrices (needs the dependency decision in the linked issue)
3 web_summary.html

Two unrelated pieces from the same work are already separable and do not touch
any of this, so I will open them regardless of the answer here: an EmptyDrops
Good-Turing fidelity fix, and barcode-setup validation.

Those two are pushed and independently reviewed, if it helps to see the standard
the CellRanger-compat work would be held to:
iandriver/rustar-aligner@fix/emptydrops-ambient-species and
@feat/solo-setup-validation, both based on 509129a.

主要言語
Rust
スター
91
フォーク
9
平均マージ
16時間 43分
マージ済み PR（30日）
22

環境構築

はじめの一歩

  1. issue を最後まで読み、次にプロジェクトのコントリビューションガイドを読みます。
  2. 着手することを issue にコメントします — 二人が同じ作業をするのを防げます。
  3. リポジトリをフォークし、ブランチを切って変更します。
  4. issue 番号を参照したプルリクエストを送ります。

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