BlackSTAR 2.7.11b-blackstar.2

BlackSTAR 2.7.11b-blackstar.2

BlackSTAR 2.7.11b-blackstar.2 promotes the cumulatively qualified
high-thread alignment stack while retaining all accepted blackstar.1
index-generation, genome-insert, integrity, and deployment capabilities.

Alignment Changes

• Recover the full allowed CPU-place union before STAR creates alignment
  pthreads when explicit OpenMP binding narrowed the initial thread.
• Select smaller record-safe input chunks automatically at 64 or more mapping
  threads.
• Interleave eligible high-thread private genome allocations across available
  NUMA memory nodes while preserving inherited policies and shared-memory
  behavior.
• Avoid redundant transcript-state copies on nonmutating recursive branches.

The STAR command and output interface is unchanged. New controls include
--readChunkSizeBytes and
--genomeLoadNumaPolicy Auto|Default|Interleave.

Qualified Performance

Three seeded order-balanced pairs used public GRCh38, Ensembl 114 annotations,
12,768,316 paired 76-base ENCODE reads, local SSD, gene counts, and 96
requested logical CPUs.

Input	blackstar.1	blackstar.2 source	Median paired improvement
Uncompressed	84.28 s	56.17 s	33.20%
zcat	90.61 s	64.03 s	28.54%

All six full-corpus comparisons preserved timing-independent final metrics,
splice junctions, and gene counts. Median peak RSS fell by approximately 6.8%.

These measurements apply to the tested host, corpus, index, storage, and
thread count; they are not universal performance guarantees.

Safety and Compatibility

• Shared-index LoadAndKeep and LoadAndRemove lifecycle passed.
• Unsorted BAM canonical records were exact.
• The inherited OpenMP-binding failure mode was reproduced and corrected with
  exact timing-independent outputs.
• Eight focused ASan/UBSan scripts passed.
• All 24 genome-insert hardening checks passed.
• All four SAindex strategy and identity checks passed.
• A conventional full BlackSTAR index aligned compatibly under official
  upstream STAR 2.7.11b.
• Two independent clean release-package builds were required to reproduce
  exact binary, archive, and provenance outputs before publication.

Retained Capabilities

• Memory-adaptive parallel full-index construction.
• Deterministic bounded SAindex and junction indexing.
• Persistent Full, Overlay, and Delta named-sequence insertion.
• Insert-only GTF annotations.
• Strict package identity, corruption rejection, and atomic publication.
• Checksum-pinned candidate selection and rollback.

Explicit Exclusions

This release does not include alignReadsMulti, persistent prefork workers,
threaded BAM-compression prototypes, A01 touched-bin reset, A02b
producer/consumer queue, or A09 LTO/PGO variants.

Platform

The qualified release target is x86-64 Linux with an OpenMP runtime
(libgomp or libomp). macOS, non-x86-64 platforms, long-read performance,
single-end performance, network-storage performance, and BAM-sorting
performance were not recertified for this release.

Artifacts

The GitHub release publishes:

• STAR;
• blackstar-2.7.11b-blackstar.2-linux-x86_64.tar.gz;
• the archive checksum sidecar;
• build-info.tsv; and
• ldd.txt.

Use the published SHA-256 metadata and build-info.tsv to pin the executable.
Publication does not authorize integration into an external production
pipeline.

Published Artifact SHA-256

• Release commit: d6fbf932ae2b155ce4f689bce106429ab2bc07f6
• STAR: 5d547c4a3ef69893fe5aa0613957448516b95b03eb17fb0e7c46348a13074202
• blackstar-2.7.11b-blackstar.2-linux-x86_64.tar.gz: 0d35930835686ae440206f378a6ea086fb2e600eb0a21583fddfefcf2b882565
• archive checksum sidecar: a650f62dcb4238ac3884348817a10b8f4cb0e1ae240573cbb150ca053be9d96e
• build-info.tsv: d7d908f2285ef14117d55d3394b8dcbae444dd12b88455af99b55172e2b17520
• ldd.txt: d386f16d2daf2ec8d94dfc714450ed3d2a81750d4539d6e0423f1a910cbeebff