Release Notes
Added
- Deterministic, shared barcode correction for every ordinary-RNA filtering
mode, multi-sample RNA, and ATAC. Cell barcodes support unique and
abundance-weighted frequency policies with Hamming-1 or the historical
substitution-or-shift neighbourhood; sample barcodes additionally support
exact correction.
- A versioned
correction_plan.bin handoff that records GPL's accepted
observed-barcode decisions. Collation and ATAC sorting apply the compiled
decisions directly while retaining explicit fallbacks for older GPL output.
- Bounded, Snappy-compressed spill and replay for the structurally ambiguous
sample-Frequency cases, controlled by --memory-limit and --tmp-dir.
- User-selectable cell and sample Frequency confidence thresholds, exact
rational comparisons, correction diagnostics, and corrected
permit_freq.bin aggregation.
Changed
- Single- and multi-barcode collation now use libradicl's bounded parallel
engines. Their hot paths fuse correction and bucket routing into one lookup,
preserve hierarchical sample/cell output, and fully order manifests.
- Requests below two threads warn and continue with two. Collation and GPL
memory requests below 256 MiB likewise warn and continue with 256 MiB.
- Legacy
--sample-correction-mode, --max-records, and --collation-mode
spellings remain accepted but are hidden from normal help.
- Quantification reuses sparse scratch storage and equivalence-class state;
bootstrap and summary-stat handling were corrected, and release builds abort
rather than unwind on panic.
Performance
- On the 1.995-billion-record Flex v2 benchmark, bounded worker-local barcode
counts and private AHash execution maps reduced GPL median wall time from
31.39 to 9.35 seconds and peak RSS from 1,735.5 to 1,550.2 MiB while
producing byte-identical correction artifacts.
- The optimized compiled-plan collators reduced measured Flex collation wall
time by 10.5% and single-barcode PBMC collation by 6.8% relative to their
immediate baselines. ATAC sorting improved by 5.3% on the measured
28.4-million-record input with byte-identical BED output.
Install alevin-fry 0.18.0
Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/alevin-fry/releases/download/v0.18.0/alevin-fry-installer.sh | sh
Download alevin-fry 0.18.0
