solo: --soloOutLayout CellRanger, CellRanger's output shape (changes output paths on 10x, stacked on #176)

CHANGELOG.md

@@ -13,6 +13,27 @@ Sections commonly used: Features, Bug fixes, Other changes.
 
 ### Features
 
+- `--soloOutLayout CellRanger` writes the solo matrices in the shape
+  `cellranger count` produces: `outs/raw_feature_bc_matrix/` and
+  `outs/filtered_feature_bc_matrix/`, gzipped, with a `-1` GEM-well suffix
+  on every barcode and one raw column per observed barcode. It implies
+  `--soloOutGzip yes`, `--soloOutRawBarcodes Observed` and an `outs/`
+  output directory, each still overridable on the command line. Counts are
+  unchanged. It is the default on 10x geometry, which **changes where
+  output files are written** on those runs; see `DIVERGENCE.md` §3.3.
+
+- On 10x geometry (`CB_UMI_Simple`, a whitelist, 16 bp CB, 10 or 12 bp
+  UMI), the five CellRanger-matching flags now **default** to their
+  CellRanger values. Any flag named on the command line wins, and the
+  substitution is logged. **This changes default output on 10x runs** and
+  diverges from STARsolo; see `DIVERGENCE.md` §1.3.
+
+- `--soloOutRawBarcodes Observed` writes the raw matrix with one column
+  per *observed* barcode instead of one per whitelist barcode, matching
+  what CellRanger's `raw_feature_bc_matrix` contains. Counts are
+  unchanged; on a 200-cell run `barcodes.tsv` goes from 62 MB to 3.4 kB.
+  **Not a STAR parameter**; default `Whitelist` keeps STARsolo behaviour.
+
 - **STARsolo single-cell quantification (`--soloType`)** — the 10x
   Chromium / plate-based count-matrix pipeline, ported from STAR and
   verified against real STARsolo (#90).
@@ -99,6 +120,12 @@ Sections commonly used: Features, Bug fixes, Other changes.
 
 ### Bug fixes
 
+- `--soloUMIfiltering MultiGeneUMI_CR` kept every gene tied at the
+  highest read count; CellRanger gives a tied UMI to no gene at all.
+  Since one read per gene is the ordinary shape of a multi-gene UMI, the
+  flag removed nothing in practice. On a 20k-read 10x fixture the count
+  matrix moves from 16 465 to 15 414 against STAR's 15 423.
+
 - **STARsolo `Gene` assignment now requires exon concordance**, matching
   STARsolo: a read counts toward a gene only when every aligned block
   lies within the gene's exons, rather than merely overlapping one. This

Cargo.toml

@@ -68,6 +68,9 @@ noodles-bgzf = { version = "0.49", features = ["libdeflate"] }
 
 [dev-dependencies]
 assert_cmd = "2"
+# Already a runtime dependency at the same version; listed here so the
+# integration tests can read the gzipped CellRanger-layout matrix files.
+flate2 = { version = "1", default-features = false, features = ["zlib-rs"] }
 predicates = "3"
 
 [build-dependencies]

DIVERGENCE.md

@@ -65,6 +65,99 @@ On the 10k yeast PE benchmark, 4 reads differ in alignment score (AS) because ST
 
 ---
 
+### 1.3 CellRanger behaviour is the default on 10x geometry
+
+**What STAR does.** STARsolo's defaults are its own (`1MM_multi`,
+`1MM_All`, no UMI filtering, `Hamming` clipping, `outFilterScoreMin 0`)
+whatever the barcode geometry. Matching CellRanger requires passing five flags,
+listed in STAR's `docs/STARsolo.md`.
+
+**What rustar-aligner does.** When the run is unambiguously 10x —
+`CB_UMI_Simple`, a whitelist, a 16-base CB and a 10- or 12-base UMI — those
+five flags default to their CellRanger values. Any flag given on the command
+line wins, and the substitution is logged in full.
+
+**Why.** A user aligning 10x data and comparing against CellRanger otherwise
+gets a successful run and different numbers, with nothing pointing at the five
+flags that explain it. Measured against CellRanger 10.0.0 on a 20 000-read
+fixture, those flags move the count matrix from 8.96% above CellRanger to
+0.03% above it, once #165's `cbMinP` posterior threshold is also applied.
+STAR 2.7.11b with the same flags is at +0.09%, so all three agree to within a
+fraction of a percent.
+
+**Impact.** This is a **change of default output behaviour** and therefore the
+largest divergence in this file. It is confined to a geometry nothing else in
+common use shares, it is escapable by naming any flag explicitly, and it is
+announced at `INFO` on every run it touches. It needs maintainer sign-off.
+
+**Source.** `src/params/mod.rs` (`looks_like_10x`,
+`apply_cellranger_defaults_on_10x`). STAR: `docs/STARsolo.md`, "Matching
+CellRanger 4.x and 5.x results".
+
+---
+
+### 3.2 `--soloOutRawBarcodes Observed` (opt-in, non-STAR)
+
+**What STAR does.** STARsolo's raw matrix has one column per whitelist
+barcode, whether or not any read carried it. For 10x v3 that is 3 686 400
+columns and a 62 MB `barcodes.tsv`, nearly all of it zeros.
+
+**What rustar-aligner does.** The same, by default. `--soloOutRawBarcodes
+Observed` narrows the raw matrix to the barcodes that actually hold a count,
+which is what CellRanger's `raw_feature_bc_matrix` contains. On a 200-cell
+fixture that is 200 columns and a 3.4 kB `barcodes.tsv`.
+
+**Why.** Someone comparing our raw matrix against CellRanger's finds no
+overlapping keys at all, because the two files mean different things by "raw".
+The flag makes the comparison possible without changing what STARsolo users
+get.
+
+**Impact.** The counts are identical either way — same entries, same values,
+verified on the fixture — only the columns present differ. This is a non-STAR
+flag and needs maintainer sign-off; it is off by default so STARsolo parity is
+untouched.
+
+**Source.** `src/solo/count.rs` (`observed_barcodes`), `src/params/mod.rs`
+(`solo_out_raw_barcodes`). CellRanger: `outs/raw_feature_bc_matrix/` from a
+`cellranger count` run, observed directly rather than taken from its source.
+
+---
+
+### 3.3 `--soloOutLayout CellRanger` (non-STAR; on by default on 10x geometry)
+
+**What STAR does.** STARsolo writes
+`Solo.out/<feature>/{raw,filtered}/{matrix.mtx, barcodes.tsv, features.tsv}`,
+uncompressed, with bare barcodes.
+
+**What rustar-aligner does.** The same, by default, on non-10x geometry.
+`--soloOutLayout CellRanger` writes the same numbers in the shape
+`cellranger count` produces: `outs/{raw,filtered}_feature_bc_matrix/`, all three
+files gzipped, a `-1` GEM-well suffix on every barcode, one raw column per
+observed barcode, and no per-feature subdirectory when a single feature is
+requested. It implies `--soloOutGzip yes`, `--soloOutRawBarcodes Observed` and
+`--soloOutFileNames outs/ ...`, each still overridable on the command line.
+
+Under §1.3 the same 10x detection turns this on by default, so a bare 10x run
+lands in CellRanger's layout.
+
+**Why.** Tools written against CellRanger's `outs/` (scanpy's `read_10x_mtx`,
+Seurat's `Read10X`, any in-house loader) key on those directory names and on
+the `-1` suffix. Without them the numbers are right and nothing downstream can
+read them without a rename step.
+
+**Impact.** No count changes: verified entry by entry on the 20 000-read
+fixture, 13 959 entries and 15 439 counts in both layouts. On 10x geometry it
+**changes where output files are written**, which needs maintainer sign-off
+alongside §1.3. Against a real `cellranger count` run on the same fixture the
+raw barcode sets match exactly, 200 of 200.
+
+**Source.** `src/solo/count.rs` (`write_gene_matrix`, `write_one_barcode`),
+`src/params/mod.rs` (`solo_out_layout`, `apply_cellranger_layout`). CellRanger:
+`outs/` from a `cellranger count` 10.0.0 run, observed directly rather than
+taken from its source.
+
+---
+
 ## 4. Implementation divergences (no intended output difference)
 
 These differ in *how* a result is produced, not *what* is produced. They are documented so a reviewer chasing a discrepancy knows the mechanism differs by design.