BlackSTAR 1.1.0

BlackSTAR 1.1.0

BlackSTAR 1.1.0 broadens the qualified BlackSTAR runtime beyond the original
paired short-read workflow and hardens release portability, memory policy, and
named-sequence insertion.

Highlights

• Adds deterministic TranscriptomeSAM primary selection across thread
  schedules while preserving the complete transcript alignment set, genomic
  BAM records, counts, junctions, and inherited downstream random state.
• Makes automatic index strategies honor cgroup-aware memory limits.
• Restores inherited NUMA policy after eligible private genome loading.
• Hardens SAM-input chunk sizing and genome-insert annotation, namespace,
  package-identity, relocation, and corruption checks.
• Isolates STAR and STARlong build state and qualifies a real direct-RNA
  STARlong fixture.
• Publishes separately labeled baseline x86-64 and AVX2 packages, with explicit
  ISA inspection and output-equivalence tests.

Cross-Workload Qualification

The Q02 matrix compared BlackSTAR with official STAR 2.7.11b across fragmented
paired and single-end RNA-seq, two-pass mapping, BySJout, chimeric detection,
coordinate-sorted BAM, transcriptome BAM, STARsolo, STARlong, SAM input, WASP,
shared-memory lifecycle, and transformed-genome output.

All 36 public pair-level output comparisons and all 12 specialized differential
checks passed. Replicated gains were observed for paired 150-base reads,
BySJout, chimeric detection, and STARlong. Other qualified rows preserve their
published variability and claim boundaries.

Limitations

• The single-end timing series preserved outputs and passed noninferiority but
  exceeded its variability gate; BlackSTAR makes no single-end speed claim.
• STARsolo and TranscriptomeSAM were noninferior, not demonstrably faster.
• The accepted STARlong fixture requires the same raised seedPerReadNmax in
  both official STAR and BlackSTAR; both inherit a failure under the default.
• Performance evidence covers x86-64 Linux, local storage, the recorded
  fixtures, and primarily high thread counts. It is not a universal guarantee.
• Overlay and Delta remain BlackSTAR-specific and require
  --genomeLoad NoSharedMemory.

Compatibility

The compatibility base remains official STAR 2.7.11b and conventional genome
format 2.7.4a. The legacy STAR --version token remains
2.7.11b-blackstar.3; STAR --version-json reports BlackSTAR 1.1.0.

Release publication does not authorize integration into an external production
pipeline.

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

BlackSTAR 1.0.0

BlackSTAR 1.0.0

BlackSTAR 1.0.0 establishes BlackSTAR as an independently maintained,
performance-oriented successor derived from STAR 2.7.11b.

Project Contract

• Independent semantic release versioning.
• Explicit STAR compatibility-base and genome-format identities.
• Maintainer-led governance, security, support, and contribution policies.
• Dedicated issue intake for upstream-origin behavior, BlackSTAR regressions,
  compatibility, and performance.
• Protected main development and reproducible release publication.

BlackSTAR remains unofficial and is not affiliated with or endorsed by the
original STAR authors.

Runtime and Compatibility

The STAR executable name and qualified command-line behavior remain
available. The transitional STAR --version token remains STAR-shaped for
wrapper compatibility; STAR --version-json reports the independent release,
compatibility base, executable identity, and genome format.

No alignment, index algorithm, or genome-insert behavior changed solely for the
independence transition. BlackSTAR 1.0.0 carries the qualified .2 runtime:

• deterministic parallel full-index construction;
• Full, Overlay, and Delta named-sequence insertion with GTF support;
• high-thread alignment scheduling, affinity, NUMA, and transcript-copy
  improvements; and
• strict package identity, reproducible release artifacts, and rollback tools.

Direct Official STAR Comparison

On the qualified 96-thread local-SSD host:

• full CHM13 index generation used 51.44% less wall time, with 46.18% higher
  median peak RSS;
• uncompressed alignment used 33.11% less wall time;
• zcat alignment used 30.75% less wall time; and
• cold GFP/GST Delta insertion was 31.50x faster than an official STAR full
  rebuild.

These results are workload-specific. See docs/PERFORMANCE.md and the bounded
machine-readable receipts for the complete claim boundary.

Platform

The stable target is x86-64 Linux with an OpenMP runtime. Other inherited source
paths remain unqualified.

Artifacts

The release publishes the STAR executable, deterministic archive, checksum
sidecar, build metadata, linkage metadata, SPDX 2.3 SBOM, and GitHub build
provenance. The archive and release assets retain the MIT license and upstream
attribution.

Publication does not authorize integration into an external production
pipeline.

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.