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Pull requests: scverse/rustar-aligner
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perf(seed): batched prefetching MMP search — measured at 0.5%, not recommended
#186
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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perf(align): reuse cluster_seeds' window-bin map across reads (-7% median, output-neutral)
#185
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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solo: count intronic reads by default on 10x (closes 30 of the 32 points vs CellRanger, stacked on #182)
#184
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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solo: --soloCellFilter OrdMag, CellRanger's cell call (first item of #181, stacked on #180)
#182
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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solo: metrics_summary.csv under the CellRanger layout (stacked on #178)
#179
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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solo: --soloOutLayout CellRanger, CellRanger's output shape (changes output paths on 10x, stacked on #176)
#178
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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feat(solo): CellRanger behaviour by default on 10x geometry (changes default output, stacked on #175)
#176
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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fix(solo): MultiGeneUMI_CR decides ownership on corrected UMIs (stacked on #174)
#175
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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feat(solo): --soloOutRawBarcodes Observed — a CellRanger-shaped raw matrix (stacked on #173)
#174
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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fix(solo): MultiGeneUMI_CR was inert — a tied UMI goes to nobody, not everybody
#173
opened Jul 31, 2026 by
BenjaminDEMAILLE
Contributor
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test: A/B bench harness that drops rounds it could not measure honestly
#171
opened Jul 30, 2026 by
BenjaminDEMAILLE
Contributor
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refactor: drop Transcript::read_seq, a public field nothing reads
#170
opened Jul 30, 2026 by
BenjaminDEMAILLE
Contributor
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fix(test): the unmapped-reason test re-implemented the logic it was testing
#169
opened Jul 30, 2026 by
BenjaminDEMAILLE
Contributor
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perf(score): slide the splice-motif window across the junction scan (output-neutral)
#167
opened Jul 30, 2026 by
BenjaminDEMAILLE
Contributor
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solo: cbMinP posterior threshold, oneExact guard, adapter-anchored geometry (replaces #150)
#165
opened Jul 30, 2026 by
BenjaminDEMAILLE
Contributor
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genome: --genomeType SuperTranscriptome
#161
opened Jul 29, 2026 by
BenjaminDEMAILLE
Contributor
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genome: --genomeTransformOutput SAM reports original coordinates
#160
opened Jul 29, 2026 by
BenjaminDEMAILLE
Contributor
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solo: --soloFeatures Transcript3p, with --soloClusterCBfile
#158
opened Jul 29, 2026 by
BenjaminDEMAILLE
Contributor
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solo: --soloCellReadStats CB writes CellReads.stats
#157
opened Jul 29, 2026 by
BenjaminDEMAILLE
Contributor
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solo: EmptyDrops_CR on CellRanger's actual statistics (SGT ambient profile, libc++ sampler)
#156
opened Jul 29, 2026 by
BenjaminDEMAILLE
Contributor
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solo: --soloUMIfiltering MultiGeneUMI_All (closes #144)
#152
opened Jul 28, 2026 by
BenjaminDEMAILLE
Contributor
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bam: --outBAMsortingBinsN spills the coordinate sort to disk bins
#151
opened Jul 28, 2026 by
BenjaminDEMAILLE
Contributor
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chimeric: --chimMultimapNmax enumeration, and --chimFilter banGenomicN
#149
opened Jul 28, 2026 by
BenjaminDEMAILLE
Contributor
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