solo: --runMode soloCellFiltering - #159
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Cell-calls an existing raw count matrix without aligning anything, taking the raw directory and an output prefix as STAR does: `--runMode soloCellFiltering /path/to/raw/ /path/to/out/prefix`. Cell calling is a decision about a matrix, not about reads. Re-calling with different `--soloCellFilter` parameters should not mean re-aligning 400 million reads, and a matrix produced by another tool should be callable too. The matrix is streamed into the same temp-body form the align path builds, so `called_cells` and `emptydrops_called` are the identical code here and there rather than a second implementation free to drift. Counts are rounded on the way in: a multimapper matrix carries real values, and the filters work on UMI totals. `--runMode` becomes a token list, because that is what STAR's is: the mode followed by its arguments. The mode itself is now validated rather than falling back to `alignReads`, so a typo is refused instead of quietly running something else. The standalone `emptydrops` binary still exists and still carries its own copy of the algorithm, which no longer matches this one. Removing it means moving `test/solo_genefull_compare.py` and `test/solo_genefull_h5_compare.py` to the new mode first, so it is left alone here rather than broken.
This was referenced Jul 29, 2026
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* fix: --runThreadN 1 ran on every core, not on one The rayon global pool was configured only when `--runThreadN` was greater than 1. Skipping the build at 1 does not give one thread: it leaves rayon's default, which is one worker per logical core. So `--runThreadN 1` ran the whole machine. Measured on 200k reads, before: 2.44 s wall at **1300% CPU**. After: 26.23 s wall at 100% CPU. The old figure was not a fast single-threaded run, it was a sixteen-way run wearing the wrong flag. This matters beyond the flag reading falsely. A scheduler or a container given one CPU gets sixteen worker threads; on a shared machine the run oversubscribes every other job; and with a thread-caching allocator each of those threads keeps its own heap, which is the very cost the comment above this code says the pool sizing exists to avoid. It also means the project's thread-invariance checks were weaker than they read: the `--runThreadN 1` leg was not a one-thread leg. Verified now that it is one: records are byte-identical between 1 and 8 threads on 200k real reads, and byte-identical to the previous binary's output at `--runThreadN 1`. Only the `@PG` `CL:` line differs between thread counts, because it records the command line. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs(changelog): record the --runThreadN 1 fix Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * refactor: drop Transcript::read_seq, which nothing ever reads The field was filled with a full copy of the read at every finalised transcript and assigned again in four more places, and no code in the crate reads it. Not "reads it rarely": the compiler was asked, and after deleting the field every one of the 97 resulting errors is a struct literal or an assignment. There is no read site, in `src` or in tests. Measured on 200k real reads at 8 threads: about 50 transcripts are finalised per read, so removing it takes **15.1 million allocations off a 200 million total** (7.6%) and 3.87 GB of copying. Wall clock does not move, and that is worth recording rather than hiding: six interleaved rounds at 87-92% CPU idle give medians 20.90 s against 20.65 s with the direction mixed, inside the run-to-run spread. mimalloc is fast enough that seventy-five small allocations per read do not surface. The reason to remove it is that it is dead weight, not that it is slow. That number also calibrates #168 downward: if removing 7.6% of the allocations changes nothing measurable, the rest of the allocation programme is unlikely to be worth a new dependency. `Transcript::read_seq` is `pub`, so this is an API removal and needs sign-off. Nothing outside the crate can be relying on its contents being meaningful, though, since it is only ever written. Output-neutral: SAM byte-identical on 200k real reads. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs(changelog): record the Transcript::read_seq removal Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * test: an A/B harness that refuses to average over a busy machine Every perf measurement on this project needs the same three guards, and I got each of them wrong at least once in a single session: An earlier harness sampled CPU idle once, before the first run. Three separate measurements then drifted below the threshold mid-series and it kept going, leaving me to spot the contaminated rounds by eye in the output. This samples idle before and after every run, drops a round if any of the four samples falls short, and prints how many it dropped, so a median over four surviving rounds cannot be mistaken for a median over six. The check is on CPU idle rather than load average, because load average is an exponential average over minutes: it refused to measure at 2.24 on a machine whose cores were all free. It reports the spread within each side next to the difference between the medians, and says so in as many words when the difference is smaller. Two changes I measured looked like wins on medians alone and were inside the spread. Both sides run as ./rustar-aligner with --outFileNamePrefix ./ from inside their own directory, because the @pg CL: line records argv verbatim: running ./old against ./new is enough to make the output differ, which cost me two false "output is not neutral" alarms. The header documents the fourth trap, which no script can enforce: timing a total hides the part that changed. BAM writing is 1-4% of a yeast run, so a total dominated by alignment cannot resolve a change to the writer. Run the None configuration alongside and read the difference. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * feat(solo): --soloCellReadStats CB writes CellReads.stats One row per cell barcode with the fifteen counters STARsolo reports: how the barcode matched, whether the read mapped to one locus or several, whether it landed on a feature, where in the gene and on which strand, whether it was mitochondrial, and whether it reached the matrix. The per-cell UMI and gene totals come from the raw matrix rather than from the read counters, so they agree with what the matrix says by construction. Reads whose barcode never resolved are summed into a single `CBnotInPasslist` row instead of being dropped. That row is the reason the file is useful: it is the difference between "these cells look thin" and "most of the input never reached a cell at all". The region columns split by strand — an antisense read counts under `exonicAS` or `intronicAS`, never under `exonic` or `intronic`. `--genomeChrSetMitochondrial` names the chromosomes behind the `mito` column. Without it the column is zero throughout, which is honest: no chromosome was declared mitochondrial. D24 comes with it. STAR emits these rows by walking a libc++ `unordered_map`, which at these sizes is the reverse of each barcode's first appearance. That is reproduced, including across threads: the per-read accumulator merges in read order, so a threaded run writes the same file as a serial one. It stops being reproducible past the point where libc++ rehashes, since the order then depends on the bucket count. The values never differ, only which line they sit on. Recorded in docs-old/dev/divergences.md. * docs: record the CellReads.stats row order in DIVERGENCE.md Section 3.2, in the format CONTRIBUTING.md asks for. * docs(changelog): keep only this PR's entry CONTRIBUTING.md requires the description to match the code; the entries for the other themes split out of #152 belong to their own PRs. * refactor(solo): drop CellReadStats::merge, which nothing calls Reads are folded in under a mutex, so there are no per-thread partials to merge; the function was reachable only from its own test. CONTRIBUTING.md rules out shipping a function no production path reaches, and the PR description claimed its test as evidence of thread-safety that the mutex actually provides. * feat(solo): --runMode soloCellFiltering Cell-calls an existing raw count matrix without aligning anything, taking the raw directory and an output prefix as STAR does: `--runMode soloCellFiltering /path/to/raw/ /path/to/out/prefix`. Cell calling is a decision about a matrix, not about reads. Re-calling with different `--soloCellFilter` parameters should not mean re-aligning 400 million reads, and a matrix produced by another tool should be callable too. The matrix is streamed into the same temp-body form the align path builds, so `called_cells` and `emptydrops_called` are the identical code here and there rather than a second implementation free to drift. Counts are rounded on the way in: a multimapper matrix carries real values, and the filters work on UMI totals. `--runMode` becomes a token list, because that is what STAR's is: the mode followed by its arguments. The mode itself is now validated rather than falling back to `alignReads`, so a typo is refused instead of quietly running something else. The standalone `emptydrops` binary still exists and still carries its own copy of the algorithm, which no longer matches this one. Removing it means moving `test/solo_genefull_compare.py` and `test/solo_genefull_h5_compare.py` to the new mode first, so it is left alone here rather than broken. --------- Co-authored-by: Benjamin Demaille <benjamin.demaille@icloud.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
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--runMode soloCellFiltering <raw dir> <output prefix>: cell-call an existing raw count matrix without aligning anything.What changed
The mode reads
matrix.mtx,barcodes.tsvandfeatures.tsvfrom a raw directory (plain or gzipped), applies--soloCellFilter, and writes the called subset under the output prefix. No genome, no reads, no index.--runModebecomes a token list, because that is what STAR's is: the mode followed by its arguments (SoloFeature_loadRawMatrix.cppreadsrunModeIn[1]andrunModeIn[2]). The mode itself is now validated rather than falling back toalignReads, so a typo is refused instead of quietly running something else.Why
Cell calling is a decision about a matrix, not about reads. Re-calling with different
--soloCellFilterparameters should not mean re-aligning, and a matrix produced by another tool should be callable too.How it avoids a second implementation
The matrix is streamed into the same temp-body form the align path builds, so
called_cellsandemptydrops_calledare the identical code here and there rather than a copy free to drift. Counts are rounded on the way in: a--soloMultiMappersmatrix carries real values, and the cell filters work on UMI totals.Verification
Two integration tests in
tests/alignment_features.rs, run withcargo test --release --test alignment_features solo_cell_filtering:test_run_mode_solo_cell_filtering_calls_cells_from_a_raw_matrix— a 20-barcode synthetic matrix where five barcodes carry 1000 UMIs and fifteen carry 2;--soloCellFilter TopCells 5writes exactly those five, with a50 5 50matrix header and the feature list carried through.test_run_mode_solo_cell_filtering_requires_its_paths— the mode without its two paths is refused.Gate: 560 lib + 23 integration tests,
cargo clippy --all-targets -- -D warnings,cargo fmt --check, MSRV 1.89 — all green.Output-neutral for every other run mode.
Known duplication left in place
The standalone
emptydropsbinary still carries its own copy of the algorithm, which this mode supersedes. Removing it means first movingtest/solo_genefull_compare.pyandtest/solo_genefull_h5_compare.pyonto the new mode, so it is left alone here rather than broken. Happy to do that as a follow-up if you want it gone.Split out of #152 following the one-theme rule in CONTRIBUTING.md.