Phase 14: STARsolo single-cell (Gene + GeneFull, EmptyDrops_CR, CellRanger matching)#90

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iandriver:phase14-starsolo

Commits on Jun 13, 2026

Phase 14: STARsolo single-cell support (MVP + CellRanger matching)

Ian Driver
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claude
committed

Commits on Jun 15, 2026

solo: buffered matrix output + per-cell build_matrix + 3-way benchmark

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Ian Driver
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solo: stream count matrix to temp file (Step 2; bounded output memory)

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Ian Driver
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Merge branch 'main' into phase14-starsolo
iandriver
authored
index: mmap the SA + SAindex on load (reclaimable, no OOM)

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Ian Driver
committed

Commits on Jun 16, 2026

index: mmap the genome too, compute reverse-complement on access (Phase 2)

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Ian Driver
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solo: GeneFull feature (intron-inclusive) + multi-feature output

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Ian Driver
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solo: EmptyDrops_CR cell caller (standalone Rust binary)

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Ian Driver
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test: GeneFull + EmptyDrops comparison scripts

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Ian Driver
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test: rustar-vs-CellRanger GeneFull + EmptyDrops h5 comparison

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Ian Driver
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test: strip 10x '-1' suffix in solo_genefull_compare barcode matching

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Ian Driver
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perf: implement --outSAMtype None + reuse gene-assignment scratch buffers

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Ian Driver
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fix(windows): gate mmap MADV_RANDOM behind cfg(unix)

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Ian Driver
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Commits on Jun 17, 2026

solo: CellRanger-style Summary.csv per feature + cross-tool compare

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Ian Driver
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solo: CellRanger-style region funnel (exonic/intronic/intergenic/antisense)

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Ian Driver
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solo: filtered/ cell-called matrix output + --soloOutGzip

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Ian Driver
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solo: SJ (splice-junction) feature matrix

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Ian Driver
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solo: --soloMultiMappers (Uniform/PropUnique/Rescue/EM)

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Ian Driver
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Commits on Jun 18, 2026

test: rustar-vs-STARsolo SJ + multiMapper diff harness

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Ian Driver
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solo: --soloType SmartSeq (plate-based, manifest, no UMI)

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Ian Driver
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solo: --soloType CB_UMI_Complex (multi-segment barcodes)

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Ian Driver
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solo: EmptyDrops_CR Monte-Carlo rescue in the filtered/ writer

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Ian Driver
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solo: paired-end SmartSeq (fragment counts)

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Ian Driver
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Commits on Jun 19, 2026

solo: Velocyto feature (spliced/unspliced/ambiguous) per Sullivan 2025

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Ian Driver
committed