Issues

• Shrink the 9 MB FASTQ test fixture and add a size check

  engineeringpriority: P0
  neurogenomics/carmack#132 · Filter by author NathanSkene opened on Oct 24, 2026 · M0 — Engineering foundations

• Decide PRs #129 and #130 and prune idle worktrees

  engineeringpriority: P0
  neurogenomics/carmack#131 · Filter by author NathanSkene opened on Oct 24, 2026 · M0 — Engineering foundations

• Allow two edits when matching the target index

  task
  neurogenomics/carmack#121 · Filter by author HDash opened on Sep 30, 2026

• Documentation

  epic
  neurogenomics/carmack#117 · Filter by author HDash opened on Sep 30, 2026

• BC2 whitelist has a pair one substitution apart, making that error undetectable

  bugtask
  neurogenomics/carmack#71 · Filter by author HDash opened on Sep 30, 2026

• Barcode extraction assigns a barcode to reads it cannot unambiguously resolve

  epic
  neurogenomics/carmack#67 · Filter by author HDash opened on Sep 30, 2026

• Downstream BAM and FASTQ stages predate the annotated-read contract

  epic
  neurogenomics/carmack#65 · Filter by author HDash opened on Sep 30, 2026

• Worker pool forks while a rich progress-bar refresh thread is running

  task
  neurogenomics/carmack#62 · Filter by author HDash opened on Sep 30, 2026
  1

• --hide_progress does nothing: the flag is stored on ctx.obj and never read

  bugtask
  neurogenomics/carmack#61 · Filter by author HDash opened on Sep 30, 2026

• Pipeline memory and throughput at production scale

  epic
  neurogenomics/carmack#35 · Filter by author HDash opened on Sep 30, 2026

• MultiQC-ready reporting across carmack stages

  epic
  neurogenomics/carmack#32 · Filter by author HDash opened on Sep 30, 2026