STAR-Cross 0.0.1: release automation, genomeGenerate perf (#2687), WASP-in-SAM (#2617), CodeQL fix

.github/codeql/codeql-config.yml

@@ -4,9 +4,10 @@ name: STAR CodeQL configuration
 # Issues in bundled libraries (htslib, SIMDe, opal, SGT) must be tracked
 # and fixed upstream; scanning them produces noise, not actionable findings.
 paths-ignore:
-  - source/htslib           # bundled HTSlib 1.21 (upstream: samtools/htslib)
+  - '**/htslib/**'          # bundled HTSlib 1.21 (upstream: samtools/htslib)
   - source/SimpleGoodTuring # bundled SGT implementation
-  - source/build            # CMake build tree — contains FetchContent deps (parasail, doctest, zlib)
+  - '**/build/**'           # CMake build tree
+  - '**/_deps/**'           # FetchContent deps (parasail, doctest, zlib, cpp-httplib, nlohmann/json)
 
 queries:
   - uses: security-extended   # OWASP top-10 + security-and-quality suite

.github/workflows/build.yml

@@ -2,9 +2,9 @@ name: Build and Test
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
-    branches: [master]
+    branches: [main]
 
 jobs:
   build-linux:
@@ -109,3 +109,38 @@ jobs:
         with:
           name: STAR-windows-x86_64
           path: source\build\STAR.exe
+
+  # Verify the genomeGenerate suffix-array rewrite (PR #2687) produces a
+  # byte-identical index vs the baseline on main, and is deterministic across
+  # thread counts and chunk layouts.
+  validate-genome-index:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0   # need main history to build the baseline
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y zlib1g-dev ninja-build
+
+      - name: Build candidate (this branch)
+        run: |
+          cd source
+          cmake -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DSTAR_BUILD_TESTS=OFF
+          cmake --build build
+          cp build/STAR "$GITHUB_WORKSPACE/STAR_new"
+
+      - name: Build baseline (main, pre-#2687)
+        run: |
+          git worktree add /tmp/star-main origin/main
+          cd /tmp/star-main/source
+          cmake -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DSTAR_BUILD_TESTS=OFF
+          cmake --build build
+          cp build/STAR "$GITHUB_WORKSPACE/STAR_old"
+
+      - name: Genome-index equivalence (old vs new, 1 vs 16 threads, multi-chunk)
+        run: |
+          chmod +x extras/tests/scripts/validate_genome_equivalence.sh
+          extras/tests/scripts/validate_genome_equivalence.sh "$GITHUB_WORKSPACE/STAR_old" "$GITHUB_WORKSPACE/STAR_new"

.github/workflows/codeql.yml

@@ -2,9 +2,9 @@ name: CodeQL Security Analysis
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
-    branches: [master]
+    branches: [main]
   schedule:
     - cron: '0 6 * * 1'  # Weekly Monday 6am UTC
 

.github/workflows/release.yml

@@ -6,7 +6,7 @@ on:
   workflow_dispatch:
     inputs:
       tag_name:
-        description: 'Release tag (e.g. v2.7.11c). Leave blank to auto-generate from commit hash.'
+        description: 'Release tag (e.g. v0.0.1). Leave blank to auto-generate from commit hash.'
         required: false
         default: ''
 
@@ -184,14 +184,14 @@ jobs:
             echo "tag=${{ inputs.tag_name }}" >> $GITHUB_OUTPUT
           else
             SHORT_SHA=$(git rev-parse --short HEAD)
-            echo "tag=2.7.11c_${SHORT_SHA}" >> $GITHUB_OUTPUT
+            echo "tag=0.0.1_${SHORT_SHA}" >> $GITHUB_OUTPUT
           fi
 
       - name: Create GitHub Release
         uses: softprops/action-gh-release@v3
         with:
           tag_name: ${{ steps.tag.outputs.tag }}
-          name: STAR ${{ steps.tag.outputs.tag }}
+          name: STAR-Cross ${{ steps.tag.outputs.tag }}
           generate_release_notes: true
           files: |
             STAR-linux-x86_64

README.md

@@ -1,15 +1,16 @@
-STAR 2.7.11c (Community Fork)
+STAR-Cross (Community Fork of STAR)
 ==========
 Spliced Transcripts Alignment to a Reference
 © Alexander Dobin, 2009-2024
 https://www.ncbi.nlm.nih.gov/pubmed/23104886
 
 > **Fork Notice:** The upstream STAR repository (`alexdobin/STAR`) appears to be unmaintained as of 2025
 > (see [community discussion](https://www.reddit.com/r/bioinformatics/comments/1joyd0p/the_star_aligner_is_unmaintained_now/)).
-> This fork maintains full output compatibility with STAR 2.7.11b while adding **Windows native support**,
-> **macOS ARM (Apple Silicon) support**, and upstream bug fixes.
-> All changes are validated to produce byte-identical results to the original 2.7.11b release.
-> Release binaries are versioned as `2.7.11c_<commit>` for traceability.
+> **STAR-Cross** is a cross-platform community fork derived from STAR 2.7.11c. It maintains output
+> compatibility with STAR 2.7.11b while adding **Windows native support**, **macOS ARM (Apple Silicon)
+> support**, **big-endian support**, **referenceless CRAM output**, and upstream bug/perf fixes.
+> Alignment output is validated to be byte-identical to the original 2.7.11b release.
+> Releases start at **v0.0.1**; the binary reports its version as `STAR-Cross 0.0.1_<commit>`.
 
 ORIGINAL AUTHOR
 ===============
@@ -338,6 +339,7 @@ FORK CHANGES
   * **Big-endian support** (`source/byteOrder.h`): the genome, suffix array and packed arrays are accessed as a little-endian byte stream regardless of host byte order, fixing the "next index is smaller than previous" failure on big-endian hosts (s390x, ppc64). Guarded so little-endian builds keep the native single-instruction load (zero performance/behavior change); only known big-endian compiles take the portable byte-wise path. Ported from the patch in upstream issue #2690. *Compile-validated only — no big-endian runner in CI.*
 
 ### Performance Optimizations
+  * Multicore `genomeGenerate` suffix-array build (upstream PR #2687): parallel prefix-bucketed chunk sort with sub-binning, optional in-memory chunk retention, and a "skip first word" comparator fast-path. Index output is **byte-identical** to the previous builder (verified in CI across thread counts and chunk layouts via `extras/tests/scripts/validate_genome_equivalence.sh`). Reconciled with the big-endian-safe comparator and MSVC (no native `__uint128`).
   * MSVC compiler: `/O2 /Ob2 /Oi /GL` with `/LTCG` link-time optimization (Windows)
   * SRW locks replacing CRITICAL_SECTION (faster mutex, Windows)
   * 4MB ifstream read buffer for FASTQ input (Windows)
@@ -357,6 +359,7 @@ FORK CHANGES
     - Trim stitched transcripts to the junction-relevant side before rescoring
     - Fix cross-mate `roStart` computation (`a2.Lread` instead of `a1.Lread` on negative strand)
   * macOS: spawn `readFilesCommand` via `posix_spawnp` instead of `vfork()`+`execlp()`+`exit()`, fixing "Failed spawning readFilesCommand" with gzipped input on macOS (upstream issue #2663). Avoids the undefined behavior of calling `exit()` in a `vfork` child. POSIX-only path; the Windows `system()`-based path is unchanged.
+  * Allow the WASP `vW:i` tag in SAM output, not just BAM (upstream PR #2617): `--waspOutputMode` no longer requires `--outSAMtype BAM`, and `vW` is emitted in the SAM/CRAM paths.
 
 ### Project Quality
   * C++17 standard (upgraded from C++11)