Issues

• 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

• TranscriptomeSAM projects ~67% more reads than STAR on human data

  scverse/rustar-aligner#292 · Filter by author BenjaminDEMAILLE opened on Oct 8, 2026

• BufferedSamRecords::new() reserves 10,000 records per read

  scverse/rustar-aligner#280 · Filter by author BenjaminDEMAILLE opened on Sep 29, 2026

• Single-end --chimOutType WithinBAM fails with "read length-sequence length mismatch"

  bug
  scverse/rustar-aligner#279 · Filter by author BenjaminDEMAILLE opened on Sep 29, 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

• Read other compressed input formats (bz2 / zstd / xz): evaluate niffler

  dependencies
  scverse/rustar-aligner#218 · Filter by author BenjaminDEMAILLE opened on Aug 7, 2026
  1

• GzDecoder truncates multi-member gzip input: reads are silently dropped

  bug
  scverse/rustar-aligner#217 · Filter by author BenjaminDEMAILLE opened on Aug 7, 2026

• Audit: does DashMap/HashMap iteration order in the splice-junction path reach any output?

  bug
  scverse/rustar-aligner#210 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026
  1

• 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

• deps: noodles 0.113 -> 0.115 and noodles-bgzf 0.49 -> 0.51 (local thread pools, with_worker_count)

  dependencies
  scverse/rustar-aligner#207 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026

• --limitBAMsortRAM aborts instead of spilling: evaluate an external sort for coordinate-sorted BAM

  enhancement
  scverse/rustar-aligner#206 · Filter by author BenjaminDEMAILLE opened on Aug 5, 2026
  1

• 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

• CellRanger4 + clip5pNbases/clip3pNbases misplaces reads by clip5pNbases

  bug
  scverse/rustar-aligner#199 · Filter by author Psy-Fer opened on Aug 5, 2026
  2