BlackSTAR 2.7.11b-blackstar.1

BlackSTAR 2.7.11b-blackstar.1

BlackSTAR is a focused x86-64 Linux fork of STAR 2.7.11b that improves full
genome-index construction and adds persistent named-sequence insertion.

Highlights

• Multithreaded, memory-adaptive suffix-array construction for
  genomeGenerate.
• Bounded parallel SAindex construction with deterministic serial reduction
  and a constrained-memory fallback.
• Parallelized junction-indexing paths with byte-identity coverage.
• genomeInsert Full, packaged Overlay, and cached Delta modes.
• Insert-only GTF annotations for added named sequences.
• Strict artifact identity, validation, corruption detection, and atomic
  publication.
• Checksum-pinned deployment selector with an executable mapping canary,
  explicit rollback, automatic fallback, and failed-transition preservation.

Qualification

In three randomized/order-balanced CHM13v2 plus ERCC benchmark pairs,
BlackSTAR reduced mean genomeGenerate wall time from 1225.78 seconds to
619.30 seconds: a 49.48% reduction and 1.98x speedup. All 42 substantive index
file comparisons were byte-identical.

A GRCh38 plus GFP/GST Delta package was created in 50.96 seconds and passed:

• exact existing-gene and splice-junction comparisons across 24 real
  paired-end samples;
• a 2,000-read GFP/GST synthetic spike;
• an independent proper-pair GFP control;
• stock STAR compatibility for Full genome-insert output.

Delta loading has a measurable fixed startup cost. In the short-sample sweep,
mean alignment time was 62.26 seconds for the base index and 71.48 seconds for
Delta. This observation was descriptive rather than order-balanced.

GitHub CI covers the release build, OpenMP linkage, an independently built
upstream 2.7.11b compatibility oracle, focused sanitizer tests, deployment
selector tests, genome-insert acceptance, SAindex strategy equivalence, and
generated-tree cleanliness.

Release identity

• Version: 2.7.11b-blackstar.1
• Commit: 821457378fa38bfb23b061b8f11ee0a09431dda7
• Platform: x86-64 Linux
• Binary SHA-256:
  115e4964990b91292f16e163c1a5fd694d5575cbe1b9ef3be342852eb91bed6a
• Archive SHA-256:
  7c70d69fea4df412ba9280bc1edf287495b834d7254b2a4fc058b80fc295dbc4

See docs/BLACKSTAR_RELEASE.md, docs/BLACKSTAR_ACCEPTANCE.md, and
docs/BLACKSTAR_PROMOTION.md for the supported boundary, complete evidence,
known limitations, and canary/rollback procedure.