STAR-Cross 0.0.1: release automation, genomeGenerate perf (#2687), WASP-in-SAM (#2617), CodeQL fix#8
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…d-party exclusion - Set project/binary version to "STAR-Cross 0.0.1_<hash>" (CMakeLists + VERSION fallback); update version_check test regex to 0.0.1. - Release workflow: name releases "STAR-Cross", auto-tag fallback 0.0.1_<sha>. - CI branch triggers master -> main (codeql.yml). - CodeQL: mark cpp-httplib include as SYSTEM (CodeQL skips system headers — the reliable fix for the cpp/non-https-url alert in the #include'd httplib.h, which paths-ignore cannot filter for C/C++); broaden config globs to **/_deps/**. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Emit the vW WASP filtering tag in the SAM/CRAM path and drop the BAM-only restriction on --waspOutputMode and the vW attribute. Emission is scoped to ATTR_vW only (the upstream patch incorrectly shared it with vG/vA). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…bin#2687) Port the parallel prefix-bucketed suffix-array chunk sort (with sub-binning, optional in-memory chunk retention, and a skip-first-word comparator fast-path) from upstream PR alexdobin#2687. Reconciled with the fork: - funCompareSuffixesFromWord uses the big-endian-safe loadUintLE loads. - sjdbSortBucket reformulated without __uint128 (MSVC has no native 128-bit); the bucket mapping stays monotonic in the key, so the total order — and thus the final index — is unchanged. - SA chunk packing keeps the in-memory path and the binary-mode disk fallback. Index output is byte-identical to the previous builder; a new CI job (validate-genome-index) builds the main baseline and this branch and diffs the SA/SAindex/Genome across 1 vs 16 threads and a low-RAM multi-chunk layout. build.yml CI branch triggers also move master -> main. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…P-in-SAM Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
… 2.0) MSVC's OpenMP 2.0 requires signed integral index variables in `#pragma omp for`. The alexdobin#2687 ports used `uint` (64-bit) indices; switch the new parallel-for loops to int64 (genomeGenerate genome scans, genomeSAindex chunks, sjdbBuildIndex bucket count/scatter). No behavior change on GCC/Clang. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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First STAR-Cross 0.0.1 release prep. Merges to
main, then tagv0.0.1triggers the release workflow (binaries for Linux/macOS-aarch64/Windows attached on success).Changes
STAR-Cross 0.0.1_<hash>; release namedSTAR-Cross v0.0.1. Default branch renamedmaster→main(CI triggers updated).release.ymlbuilds all 3 platforms + tests and publishes binaries to the GitHub Release only if all succeed (tagv*).cpp/non-https-urlin the fetchedhttplib.h) is resolved by marking cpp-httplib as a SYSTEM include (CodeQL skips system headers —paths-ignorecan't filter headers#included into compiled TUs), plus broader config globs.__uint128). Gated by a newvalidate-genome-indexCI job that diffs the SA/SAindex/Genome produced by themainbaseline vs this branch across 1/16 threads and a low-RAM multi-chunk layout — must be byte-identical.vW:itag for wasp in SAM output alexdobin/STAR#2617: WASPvW:itag allowed in SAM output (scoped correctly to vW).Already present (verified, not re-done)
sjA/sjFilter/sjChunksmemory leaks alexdobin/STAR#2676 (SJ leak) — already fixed.posix_spawnreadFilesCommand (from fix(macOS): spawn readFilesCommand via shell (posix_spawnp) so gzipped input works alexdobin/STAR#2693), and its opal Makefile change is moot (fork uses parasail).Testing
.cppsyntax-checked against MSVC STL; Improve genomeGenerate multicore index build performance alexdobin/STAR#2687 verified on both LE and forced-BE paths.After this is green and merged, I will delete the old releases and tag
v0.0.1.