Issues

• Tracking: open PRs frozen pending maintainer review (stacks and merge order)

  scverse/rustar-aligner#324 · Filter by author BenjaminDEMAILLE opened on Oct 11, 2026

• Tracking: open PRs that conflict with main

  scverse/rustar-aligner#299 · Filter by author BenjaminDEMAILLE opened on Oct 8, 2026

• Tracking: remaining ROADMAP.md items (Phases 14, 16, 17)

  scverse/rustar-aligner#298 · Filter by author BenjaminDEMAILLE opened on Oct 8, 2026

• Tracking: PRs for #31, #95, #172, #218, #223, #270, #279, #280

  scverse/rustar-aligner#277 · Filter by author BenjaminDEMAILLE opened on Sep 29, 2026

• Consider hdf5-pure (pure-Rust HDF5) for optional .h5 output

  dependenciesfile-formats
  scverse/rustar-aligner#270 · Filter by author BenjaminDEMAILLE opened on Sep 29, 2026

• Enable performance (here speed) benchmarking

  scverse/rustar-aligner#245 · Filter by author Zethson opened on Aug 27, 2026
  

• Enable middle/larger scale dataset tests

  scverse/rustar-aligner#244 · Filter by author Zethson opened on Aug 27, 2026
  

• outFilterMismatchNoverLmax is applied to the read length, not the mapped length

  scverse/rustar-aligner#238 · Filter by author BenjaminDEMAILLE opened on Aug 26, 2026

• Dependency discussion: optional rapidgzip feature for parallel gzip input

  dependencies
  scverse/rustar-aligner#224 · Filter by author BenjaminDEMAILLE opened on Aug 11, 2026
  1

• Align pipeline stops scaling past ~4-8 threads: decode and write are each a single thread

  enhancement
  scverse/rustar-aligner#223 · Filter by author BenjaminDEMAILLE opened on Aug 11, 2026
  2

• docs: add DEPENDENCIES.md recording accepted and declined crates

  documentation
  scverse/rustar-aligner#209 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• Dependency discussion: interval-overlap crates (superintervals / coitrees / rust-lapper)

  dependencies
  scverse/rustar-aligner#208 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• Dependency discussion: portable SIMD crate (wide/pulp) vs the hand-rolled intrinsics in simd_scan.rs

  dependencies
  scverse/rustar-aligner#205 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• dev-deps: add a benchmark harness (divan or criterion) — there is no benches/ today

  dependencies
  scverse/rustar-aligner#204 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• Dependency discussion: the rust-seq crates (packed-seq, simd-minimizers, seq-hash)

  dependencies
  scverse/rustar-aligner#203 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• Dependency discussion: sufr/libsufr for suffix-array construction (vs the caps-sa incumbent)

  dependencies
  scverse/rustar-aligner#202 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• Dependency survey (Aug 2026): umbrella for the crate evaluations

  dependencies
  scverse/rustar-aligner#201 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• PR review queue: what is ready, what is stacked, what is waiting on a decision

  scverse/rustar-aligner#195 · Filter by author BenjaminDEMAILLE opened on Aug 1, 2026
  1

• CellRanger GEX pipeline: coverage map, stage by stage

  scverse/rustar-aligner#181 · Filter by author BenjaminDEMAILLE opened on Jul 31, 2026

• solo: two CellRanger-matching flags are inert, and the count matrix is 8.9% off

  scverse/rustar-aligner#172 · Filter by author BenjaminDEMAILLE opened on Jul 30, 2026
  3

• Status of development

  scverse/rustar-aligner#163 · Filter by author BDBGenomics opened on Jul 29, 2026
  1

• Dependency discussion: libsais (vendored C via cc) for suffix-array construction

  dependencies
  scverse/rustar-aligner#162 · Filter by author BenjaminDEMAILLE opened on Jul 29, 2026

• Roadmap: remaining STAR-rs port work, split by theme

  scverse/rustar-aligner#143 · Filter by author BenjaminDEMAILLE opened on Jul 28, 2026
  2

• Parallel inputs ({C,V,,}BQ or parallel readers for fastq)

  file-formats
  scverse/rustar-aligner#97 · Filter by author ilan-gold opened on Jun 25, 2026

• Output RAD output

  file-formats
  scverse/rustar-aligner#96 · Filter by author Psy-Fer opened on Jun 25, 2026