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.